7Y44 | pdb_00007y44

Re-refinement of damage free X-ray structure of bovine cytochrome c oxidase at 1.9 angstrom resolution

PDB DOI: https://doi.org/10.2210/pdb7Y44/pdb

Classification: OXIDOREDUCTASE
Organism(s): Bos taurus
Mutation(s): No
Membrane Protein: Yes PDBTM

Deposited: 2022-06-14 Released: 2022-07-20
Deposition Author(s): Tsukihara, T., Hirata, K., Ago, H.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.227 (Depositor), 0.227 (DCC)
R-Value Work:
0.185 (Depositor), 0.185 (DCC)
R-Value Observed:
0.188 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Determination of damage-free crystal structure of an X-ray-sensitive protein using an XFEL.

Hirata, K., Shinzawa-Itoh, K., Yano, N., Takemura, S., Kato, K., Hatanaka, M., Muramoto, K., Kawahara, T., Tsukihara, T., Yamashita, E., Tono, K., Ueno, G., Hikima, T., Murakami, H., Inubushi, Y., Yabashi, M., Ishikawa, T., Yamamoto, M., Ogura, T., Sugimoto, H., Shen, J.R., Yoshikawa, S., Ago, H.

(2014) Nat Methods 11: 734-736

PubMed: 24813624 Search on PubMed
DOI: https://doi.org/10.1038/nmeth.2962
Primary Citation Related Structures:
3WG7, 7Y44

PubMed Abstract:
We report a method of femtosecond crystallography for solving radiation damage-free crystal structures of large proteins at sub-angstrom spatial resolution, using a large single crystal and the femtosecond pulses of an X-ray free-electron laser (XFEL). We demonstrated the performance of the method by determining a 1.9-Å radiation damage-free structure of bovine cytochrome c oxidase, a large (420-kDa), highly radiation-sensitive membrane protein.

Organizational Affiliation

1] RIKEN SPring-8 Center, Sayo, Japan. [2] Japan Science and Technology Agency (JST), Core Research for Evolutional Science and Technology (CREST), Kawaguchi, Japan. [3].

Macromolecule Content

Total Structure Weight: 456.49 kDa
Atom Count: 34,120
Modeled Residue Count: 3,558
Deposited Residue Count: 3,614
Unique protein chains: 13

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 1	A, N	514	Bos taurus	Mutation(s): 0 EC: 7.1.1.9 Membrane Entity: Yes
UniProt
Find proteins for P00396 (Bos taurus) Explore P00396 Go to UniProtKB: P00396
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00396
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Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 2	B, O	227	Bos taurus	Mutation(s): 0 EC: 7.1.1.9 Membrane Entity: Yes
UniProt
Find proteins for P68530 (Bos taurus) Explore P68530 Go to UniProtKB: P68530
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P68530
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Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 3	C, P	261	Bos taurus	Mutation(s): 0 EC: 7.1.1.9 Membrane Entity: Yes
UniProt
Find proteins for P00415 (Bos taurus) Explore P00415 Go to UniProtKB: P00415
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00415
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Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 4 isoform 1	D, Q	147	Bos taurus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P00423 (Bos taurus) Explore P00423 Go to UniProtKB: P00423
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00423
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 5A	E, R	109	Bos taurus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P00426 (Bos taurus) Explore P00426 Go to UniProtKB: P00426
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00426
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Reference Sequence

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 5B, mitochondrial	F, S	98	Bos taurus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P00428 (Bos taurus) Explore P00428 Go to UniProtKB: P00428
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UniProt Group	P00428
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Reference Sequence

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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 6A2	G, T	85	Bos taurus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P07471 (Bos taurus) Explore P07471 Go to UniProtKB: P07471
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UniProt Group	P07471
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Reference Sequence

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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 6B1	H, U	85	Bos taurus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P00429 (Bos taurus) Explore P00429 Go to UniProtKB: P00429
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00429
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Reference Sequence

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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 6C	I, V	73	Bos taurus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P04038 (Bos taurus) Explore P04038 Go to UniProtKB: P04038
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UniProt Group	P04038
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Reference Sequence

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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 7A1	J, W	59	Bos taurus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P07470 (Bos taurus) Explore P07470 Go to UniProtKB: P07470
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UniProt Group	P07470
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Reference Sequence

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Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 7B	K, X	56	Bos taurus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P13183 (Bos taurus) Explore P13183 Go to UniProtKB: P13183
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UniProt Group	P13183
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Reference Sequence

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Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 7C, mitochondrial	L, Y	47	Bos taurus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P00430 (Bos taurus) Explore P00430 Go to UniProtKB: P00430
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00430
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Reference Sequence

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Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 8B	M, Z	46	Bos taurus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P10175 (Bos taurus) Explore P10175 Go to UniProtKB: P10175
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UniProt Group	P10175
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Reference Sequence

Small Molecules

Ligands 16 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CDL Query on CDL Download:Ideal Coordinates CCD File SDF format, chain KE [auth T] SDF format, chain ND [auth P] SDF format, chain PB [auth G] SDF format, chain ZA [auth C] MOL2 format, chain KE [auth T] MOL2 format, chain ND [auth P] MOL2 format, chain PB [auth G] MOL2 format, chain ZA [auth C] mmCIF format, chain KE [auth T] mmCIF format, chain ND [auth P] mmCIF format, chain PB [auth G] mmCIF format, chain ZA [auth C]	KE [auth T], ND [auth P], PB [auth G], ZA [auth C]	CARDIOLIPIN C₈₁ H₁₅₆ O₁₇ P₂ XVTUQDWPJJBEHJ-KZCWQMDCSA-L		Interactions Focus chain KE [auth T] Focus chain ND [auth P] Focus chain PB [auth G] Focus chain ZA [auth C] Interactions & Density Focus chain KE [auth T] Focus chain ND [auth P] Focus chain PB [auth G] Focus chain ZA [auth C]
TGL Query on TGL Download:Ideal Coordinates CCD File SDF format, chain CC [auth L] SDF format, chain DD [auth O] SDF format, chain IB [auth D] SDF format, chain QA [auth B] SDF format, chain VE [auth Y] SDF format, chain YD [auth Q] MOL2 format, chain CC [auth L] MOL2 format, chain DD [auth O] MOL2 format, chain IB [auth D] MOL2 format, chain QA [auth B] MOL2 format, chain VE [auth Y] MOL2 format, chain YD [auth Q] mmCIF format, chain CC [auth L] mmCIF format, chain DD [auth O] mmCIF format, chain IB [auth D] mmCIF format, chain QA [auth B] mmCIF format, chain VE [auth Y] mmCIF format, chain YD [auth Q]	CC [auth L] DD [auth O] IB [auth D] QA [auth B] VE [auth Y] CC [auth L], DD [auth O], IB [auth D], QA [auth B], VE [auth Y], YD [auth Q]	TRISTEAROYLGLYCEROL C₅₇ H₁₁₀ O₆ DCXXMTOCNZCJGO-UHFFFAOYSA-N		Interactions Focus chain CC [auth L] Focus chain DD [auth O] Focus chain IB [auth D] Focus chain QA [auth B] Focus chain VE [auth Y] Focus chain YD [auth Q] Interactions & Density Focus chain CC [auth L] Focus chain DD [auth O] Focus chain IB [auth D] Focus chain QA [auth B] Focus chain VE [auth Y] Focus chain YD [auth Q]
HEA Query on HEA Download:Ideal Coordinates CCD File SDF format, chain AA [auth A] SDF format, chain BA [auth A] SDF format, chain JC [auth N] SDF format, chain KC [auth N] MOL2 format, chain AA [auth A] MOL2 format, chain BA [auth A] MOL2 format, chain JC [auth N] MOL2 format, chain KC [auth N] mmCIF format, chain AA [auth A] mmCIF format, chain BA [auth A] mmCIF format, chain JC [auth N] mmCIF format, chain KC [auth N]	AA [auth A], BA [auth A], JC [auth N], KC [auth N]	HEME-A C₄₉ H₅₆ Fe N₄ O₆ ZGGYGTCPXNDTRV-PRYGPKJJSA-L		Interactions Focus chain AA [auth A] Focus chain BA [auth A] Focus chain JC [auth N] Focus chain KC [auth N] Interactions & Density Focus chain AA [auth A] Focus chain BA [auth A] Focus chain JC [auth N] Focus chain KC [auth N]
PEK Query on PEK Download:Ideal Coordinates CCD File SDF format, chain CB [auth C] SDF format, chain EB [auth C] SDF format, chain LD [auth P] SDF format, chain QB [auth G] SDF format, chain QD [auth P] SDF format, chain XA [auth C] MOL2 format, chain CB [auth C] MOL2 format, chain EB [auth C] MOL2 format, chain LD [auth P] MOL2 format, chain QB [auth G] MOL2 format, chain QD [auth P] MOL2 format, chain XA [auth C] mmCIF format, chain CB [auth C] mmCIF format, chain EB [auth C] mmCIF format, chain LD [auth P] mmCIF format, chain QB [auth G] mmCIF format, chain QD [auth P] mmCIF format, chain XA [auth C]	CB [auth C] EB [auth C] LD [auth P] QB [auth G] QD [auth P] CB [auth C], EB [auth C], LD [auth P], QB [auth G], QD [auth P], XA [auth C]	(1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE C₄₃ H₇₈ N O₈ P ANRKEHNWXKCXDB-BHFWLYLHSA-N		Interactions Focus chain CB [auth C] Focus chain EB [auth C] Focus chain LD [auth P] Focus chain QB [auth G] Focus chain QD [auth P] Focus chain XA [auth C] Interactions & Density Focus chain CB [auth C] Focus chain EB [auth C] Focus chain LD [auth P] Focus chain QB [auth G] Focus chain QD [auth P] Focus chain XA [auth C]
PSC Query on PSC Download:Ideal Coordinates CCD File SDF format, chain QC [auth N] SDF format, chain SA [auth B] MOL2 format, chain QC [auth N] MOL2 format, chain SA [auth B] mmCIF format, chain QC [auth N] mmCIF format, chain SA [auth B]	QC [auth N], SA [auth B]	(7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE C₄₂ H₈₁ N O₈ P JLPULHDHAOZNQI-AUSZDXHESA-O		Interactions Focus chain QC [auth N] Focus chain SA [auth B] Interactions & Density Focus chain QC [auth N] Focus chain SA [auth B]
PGV Query on PGV Download:Ideal Coordinates CCD File SDF format, chain DB [auth C] SDF format, chain GA [auth A] SDF format, chain HA [auth A] SDF format, chain ID [auth P] SDF format, chain JD [auth P] SDF format, chain MD [auth P] SDF format, chain PC [auth N] SDF format, chain YA [auth C] MOL2 format, chain DB [auth C] MOL2 format, chain GA [auth A] MOL2 format, chain HA [auth A] MOL2 format, chain ID [auth P] MOL2 format, chain JD [auth P] MOL2 format, chain MD [auth P] MOL2 format, chain PC [auth N] MOL2 format, chain YA [auth C] mmCIF format, chain DB [auth C] mmCIF format, chain GA [auth A] mmCIF format, chain HA [auth A] mmCIF format, chain ID [auth P] mmCIF format, chain JD [auth P] mmCIF format, chain MD [auth P] mmCIF format, chain PC [auth N] mmCIF format, chain YA [auth C]	DB [auth C] GA [auth A] HA [auth A] ID [auth P] JD [auth P] DB [auth C], GA [auth A], HA [auth A], ID [auth P], JD [auth P], MD [auth P], PC [auth N], YA [auth C]	(1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE C₄₀ H₇₇ O₁₀ P ADYWCMPUNIVOEA-GPJPVTGXSA-N		Interactions Focus chain DB [auth C] Focus chain GA [auth A] Focus chain HA [auth A] Focus chain ID [auth P] Focus chain JD [auth P] Focus chain MD [auth P] Focus chain PC [auth N] Focus chain YA [auth C] Interactions & Density Focus chain DB [auth C] Focus chain GA [auth A] Focus chain HA [auth A] Focus chain ID [auth P] Focus chain JD [auth P] Focus chain MD [auth P] Focus chain PC [auth N] Focus chain YA [auth C]
DMU Query on DMU Download:Ideal Coordinates CCD File SDF format, chain AC [auth K] SDF format, chain AE [auth Q] SDF format, chain BC [auth K] SDF format, chain DC [auth L] SDF format, chain HB [auth C] SDF format, chain HC [auth M] SDF format, chain HD [auth O] SDF format, chain JB [auth D] SDF format, chain LE [auth T] SDF format, chain PA [auth A] SDF format, chain QE [auth X] SDF format, chain RE [auth X] SDF format, chain SB [auth G] SDF format, chain SE [auth X] SDF format, chain TE [auth X] SDF format, chain VA [auth B] SDF format, chain VD [auth P] SDF format, chain WB [auth K] SDF format, chain XB [auth K] SDF format, chain YB [auth K] SDF format, chain YE [auth Z] SDF format, chain ZB [auth K] SDF format, chain XD [auth P] MOL2 format, chain AC [auth K] MOL2 format, chain AE [auth Q] MOL2 format, chain BC [auth K] MOL2 format, chain DC [auth L] MOL2 format, chain HB [auth C] MOL2 format, chain HC [auth M] MOL2 format, chain HD [auth O] MOL2 format, chain JB [auth D] MOL2 format, chain LE [auth T] MOL2 format, chain PA [auth A] MOL2 format, chain QE [auth X] MOL2 format, chain RE [auth X] MOL2 format, chain SB [auth G] MOL2 format, chain SE [auth X] MOL2 format, chain TE [auth X] MOL2 format, chain VA [auth B] MOL2 format, chain VD [auth P] MOL2 format, chain WB [auth K] MOL2 format, chain XB [auth K] MOL2 format, chain YB [auth K] MOL2 format, chain YE [auth Z] MOL2 format, chain ZB [auth K] MOL2 format, chain XD [auth P] mmCIF format, chain AC [auth K] mmCIF format, chain AE [auth Q] mmCIF format, chain BC [auth K] mmCIF format, chain DC [auth L] mmCIF format, chain HB [auth C] mmCIF format, chain HC [auth M] mmCIF format, chain HD [auth O] mmCIF format, chain JB [auth D] mmCIF format, chain LE [auth T] mmCIF format, chain PA [auth A] mmCIF format, chain QE [auth X] mmCIF format, chain RE [auth X] mmCIF format, chain SB [auth G] mmCIF format, chain SE [auth X] mmCIF format, chain TE [auth X] mmCIF format, chain VA [auth B] mmCIF format, chain VD [auth P] mmCIF format, chain WB [auth K] mmCIF format, chain XB [auth K] mmCIF format, chain YB [auth K] mmCIF format, chain YE [auth Z] mmCIF format, chain ZB [auth K] mmCIF format, chain XD [auth P]	AC [auth K] AE [auth Q] BC [auth K] DC [auth L] HB [auth C] AC [auth K], AE [auth Q], BC [auth K], DC [auth L], HB [auth C], HC [auth M], HD [auth O], JB [auth D], LE [auth T], PA [auth A], QE [auth X], RE [auth X], SB [auth G], SE [auth X], TE [auth X], VA [auth B], VD [auth P], WB [auth K], XB [auth K], XD [auth P], YB [auth K], YE [auth Z], ZB [auth K]	DECYL-BETA-D-MALTOPYRANOSIDE C₂₂ H₄₂ O₁₁ WOQQAWHSKSSAGF-WXFJLFHKSA-N		Interactions Focus chain AC [auth K] Focus chain AE [auth Q] Focus chain BC [auth K] Focus chain DC [auth L] Focus chain HB [auth C] Focus chain HC [auth M] Focus chain HD [auth O] Focus chain JB [auth D] Focus chain LE [auth T] Focus chain PA [auth A] Focus chain QE [auth X] Focus chain RE [auth X] Focus chain SB [auth G] Focus chain SE [auth X] Focus chain TE [auth X] Focus chain VA [auth B] Focus chain VD [auth P] Focus chain WB [auth K] Focus chain XB [auth K] Focus chain XD [auth P] Focus chain YB [auth K] Focus chain YE [auth Z] Focus chain ZB [auth K] Interactions & Density Focus chain AC [auth K] Focus chain AE [auth Q] Focus chain BC [auth K] Focus chain DC [auth L] Focus chain HB [auth C] Focus chain HC [auth M] Focus chain HD [auth O] Focus chain JB [auth D] Focus chain LE [auth T] Focus chain PA [auth A] Focus chain QE [auth X] Focus chain RE [auth X] Focus chain SB [auth G] Focus chain SE [auth X] Focus chain TE [auth X] Focus chain VA [auth B] Focus chain VD [auth P] Focus chain WB [auth K] Focus chain XB [auth K] Focus chain XD [auth P] Focus chain YB [auth K] Focus chain YE [auth Z] Focus chain ZB [auth K]
CHD Query on CHD Download:Ideal Coordinates CCD File SDF format, chain AB [auth C] SDF format, chain BB [auth C] SDF format, chain EC [auth L] SDF format, chain JE [auth T] SDF format, chain NE [auth W] SDF format, chain OD [auth P] SDF format, chain PD [auth P] SDF format, chain RB [auth G] SDF format, chain UE [auth X] SDF format, chain VB [auth J] SDF format, chain WE [auth Y] MOL2 format, chain AB [auth C] MOL2 format, chain BB [auth C] MOL2 format, chain EC [auth L] MOL2 format, chain JE [auth T] MOL2 format, chain NE [auth W] MOL2 format, chain OD [auth P] MOL2 format, chain PD [auth P] MOL2 format, chain RB [auth G] MOL2 format, chain UE [auth X] MOL2 format, chain VB [auth J] MOL2 format, chain WE [auth Y] mmCIF format, chain AB [auth C] mmCIF format, chain BB [auth C] mmCIF format, chain EC [auth L] mmCIF format, chain JE [auth T] mmCIF format, chain NE [auth W] mmCIF format, chain OD [auth P] mmCIF format, chain PD [auth P] mmCIF format, chain RB [auth G] mmCIF format, chain UE [auth X] mmCIF format, chain VB [auth J] mmCIF format, chain WE [auth Y]	AB [auth C] BB [auth C] EC [auth L] JE [auth T] NE [auth W] AB [auth C], BB [auth C], EC [auth L], JE [auth T], NE [auth W], OD [auth P], PD [auth P], RB [auth G], UE [auth X], VB [auth J], WE [auth Y]	CHOLIC ACID C₂₄ H₄₀ O₅ BHQCQFFYRZLCQQ-OELDTZBJSA-N		Interactions Focus chain AB [auth C] Focus chain BB [auth C] Focus chain EC [auth L] Focus chain JE [auth T] Focus chain NE [auth W] Focus chain OD [auth P] Focus chain PD [auth P] Focus chain RB [auth G] Focus chain UE [auth X] Focus chain VB [auth J] Focus chain WE [auth Y] Interactions & Density Focus chain AB [auth C] Focus chain BB [auth C] Focus chain EC [auth L] Focus chain JE [auth T] Focus chain NE [auth W] Focus chain OD [auth P] Focus chain PD [auth P] Focus chain RB [auth G] Focus chain UE [auth X] Focus chain VB [auth J] Focus chain WE [auth Y]
CUA Query on CUA Download:Ideal Coordinates CCD File SDF format, chain ED [auth O] SDF format, chain RA [auth B] MOL2 format, chain ED [auth O] MOL2 format, chain RA [auth B] mmCIF format, chain ED [auth O] mmCIF format, chain RA [auth B]	ED [auth O], RA [auth B]	DINUCLEAR COPPER ION Cu₂ ALKZAGKDWUSJED-UHFFFAOYSA-N		Interactions Focus chain ED [auth O] Focus chain RA [auth B] Interactions & Density Focus chain ED [auth O] Focus chain RA [auth B]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain ME [auth U] SDF format, chain UB [auth H] MOL2 format, chain ME [auth U] MOL2 format, chain UB [auth H] mmCIF format, chain ME [auth U] mmCIF format, chain UB [auth H]	ME [auth U], UB [auth H]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain ME [auth U] Focus chain UB [auth H] Interactions & Density Focus chain ME [auth U] Focus chain UB [auth H]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain CE [auth S] SDF format, chain KB [auth F] MOL2 format, chain CE [auth S] MOL2 format, chain KB [auth F] mmCIF format, chain CE [auth S] mmCIF format, chain KB [auth F]	CE [auth S], KB [auth F]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain CE [auth S] Focus chain KB [auth F] Interactions & Density Focus chain CE [auth S] Focus chain KB [auth F]
CU Query on CU Download:Ideal Coordinates CCD File SDF format, chain CA [auth A] SDF format, chain LC [auth N] MOL2 format, chain CA [auth A] MOL2 format, chain LC [auth N] mmCIF format, chain CA [auth A] mmCIF format, chain LC [auth N]	CA [auth A], LC [auth N]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N		Interactions Focus chain CA [auth A] Focus chain LC [auth N] Interactions & Density Focus chain CA [auth A] Focus chain LC [auth N]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain AD [auth N] SDF format, chain BD [auth N] SDF format, chain BE [auth R] SDF format, chain CD [auth N] SDF format, chain DE [auth S] SDF format, chain EE [auth S] SDF format, chain FB [auth C] SDF format, chain FC [auth L] SDF format, chain FD [auth O] SDF format, chain FE [auth S] SDF format, chain GB [auth C] SDF format, chain GC [auth L] SDF format, chain GD [auth O] SDF format, chain GE [auth S] SDF format, chain HE [auth S] SDF format, chain IA [auth A] SDF format, chain IC [auth M] SDF format, chain IE [auth S] SDF format, chain JA [auth A] SDF format, chain KA [auth A] SDF format, chain LA [auth A] SDF format, chain LB [auth F] SDF format, chain MA [auth A] SDF format, chain MB [auth F] SDF format, chain NA [auth A] SDF format, chain NB [auth F] SDF format, chain OA [auth A] SDF format, chain OB [auth F] SDF format, chain OE [auth W] SDF format, chain PE [auth W] SDF format, chain RC [auth N] SDF format, chain RD [auth P] SDF format, chain SC [auth N] SDF format, chain SD [auth P] SDF format, chain TA [auth B] SDF format, chain TB [auth G] SDF format, chain TC [auth N] SDF format, chain TD [auth P] SDF format, chain UA [auth B] SDF format, chain UC [auth N] SDF format, chain UD [auth P] SDF format, chain VC [auth N] SDF format, chain WC [auth N] SDF format, chain WD [auth P] SDF format, chain XC [auth N] SDF format, chain XE [auth Y] SDF format, chain YC [auth N] SDF format, chain ZC [auth N] SDF format, chain ZD [auth Q] MOL2 format, chain AD [auth N] MOL2 format, chain BD [auth N] MOL2 format, chain BE [auth R] MOL2 format, chain CD [auth N] MOL2 format, chain DE [auth S] MOL2 format, chain EE [auth S] MOL2 format, chain FB [auth C] MOL2 format, chain FC [auth L] MOL2 format, chain FD [auth O] MOL2 format, chain FE [auth S] MOL2 format, chain GB [auth C] MOL2 format, chain GC [auth L] MOL2 format, chain GD [auth O] MOL2 format, chain GE [auth S] MOL2 format, chain HE [auth S] MOL2 format, chain IA [auth A] MOL2 format, chain IC [auth M] MOL2 format, chain IE [auth S] MOL2 format, chain JA [auth A] MOL2 format, chain KA [auth A] MOL2 format, chain LA [auth A] MOL2 format, chain LB [auth F] MOL2 format, chain MA [auth A] MOL2 format, chain MB [auth F] MOL2 format, chain NA [auth A] MOL2 format, chain NB [auth F] MOL2 format, chain OA [auth A] MOL2 format, chain OB [auth F] MOL2 format, chain OE [auth W] MOL2 format, chain PE [auth W] MOL2 format, chain RC [auth N] MOL2 format, chain RD [auth P] MOL2 format, chain SC [auth N] MOL2 format, chain SD [auth P] MOL2 format, chain TA [auth B] MOL2 format, chain TB [auth G] MOL2 format, chain TC [auth N] MOL2 format, chain TD [auth P] MOL2 format, chain UA [auth B] MOL2 format, chain UC [auth N] MOL2 format, chain UD [auth P] MOL2 format, chain VC [auth N] MOL2 format, chain WC [auth N] MOL2 format, chain WD [auth P] MOL2 format, chain XC [auth N] MOL2 format, chain XE [auth Y] MOL2 format, chain YC [auth N] MOL2 format, chain ZC [auth N] MOL2 format, chain ZD [auth Q] mmCIF format, chain AD [auth N] mmCIF format, chain BD [auth N] mmCIF format, chain BE [auth R] mmCIF format, chain CD [auth N] mmCIF format, chain DE [auth S] mmCIF format, chain EE [auth S] mmCIF format, chain FB [auth C] mmCIF format, chain FC [auth L] mmCIF format, chain FD [auth O] mmCIF format, chain FE [auth S] mmCIF format, chain GB [auth C] mmCIF format, chain GC [auth L] mmCIF format, chain GD [auth O] mmCIF format, chain GE [auth S] mmCIF format, chain HE [auth S] mmCIF format, chain IA [auth A] mmCIF format, chain IC [auth M] mmCIF format, chain IE [auth S] mmCIF format, chain JA [auth A] mmCIF format, chain KA [auth A] mmCIF format, chain LA [auth A] mmCIF format, chain LB [auth F] mmCIF format, chain MA [auth A] mmCIF format, chain MB [auth F] mmCIF format, chain NA [auth A] mmCIF format, chain NB [auth F] mmCIF format, chain OA [auth A] mmCIF format, chain OB [auth F] mmCIF format, chain OE [auth W] mmCIF format, chain PE [auth W] mmCIF format, chain RC [auth N] mmCIF format, chain RD [auth P] mmCIF format, chain SC [auth N] mmCIF format, chain SD [auth P] mmCIF format, chain TA [auth B] mmCIF format, chain TB [auth G] mmCIF format, chain TC [auth N] mmCIF format, chain TD [auth P] mmCIF format, chain UA [auth B] mmCIF format, chain UC [auth N] mmCIF format, chain UD [auth P] mmCIF format, chain VC [auth N] mmCIF format, chain WC [auth N] mmCIF format, chain WD [auth P] mmCIF format, chain XC [auth N] mmCIF format, chain XE [auth Y] mmCIF format, chain YC [auth N] mmCIF format, chain ZC [auth N] mmCIF format, chain ZD [auth Q]	AD [auth N] BD [auth N] BE [auth R] CD [auth N] DE [auth S] AD [auth N], BD [auth N], BE [auth R], CD [auth N], DE [auth S], EE [auth S], FB [auth C], FC [auth L], FD [auth O], FE [auth S], GB [auth C], GC [auth L], GD [auth O], GE [auth S], HE [auth S], IA [auth A], IC [auth M], IE [auth S], JA [auth A], KA [auth A], LA [auth A], LB [auth F], MA [auth A], MB [auth F], NA [auth A], NB [auth F], OA [auth A], OB [auth F], OE [auth W], PE [auth W], RC [auth N], RD [auth P], SC [auth N], SD [auth P], TA [auth B], TB [auth G], TC [auth N], TD [auth P], UA [auth B], UC [auth N], UD [auth P], VC [auth N], WC [auth N], WD [auth P], XC [auth N], XE [auth Y], YC [auth N], ZC [auth N], ZD [auth Q]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AD [auth N] Focus chain BD [auth N] Focus chain BE [auth R] Focus chain CD [auth N] Focus chain DE [auth S] Focus chain EE [auth S] Focus chain FB [auth C] Focus chain FC [auth L] Focus chain FD [auth O] Focus chain FE [auth S] Focus chain GB [auth C] Focus chain GC [auth L] Focus chain GD [auth O] Focus chain GE [auth S] Focus chain HE [auth S] Focus chain IA [auth A] Focus chain IC [auth M] Focus chain IE [auth S] Focus chain JA [auth A] Focus chain KA [auth A] Focus chain LA [auth A] Focus chain LB [auth F] Focus chain MA [auth A] Focus chain MB [auth F] Focus chain NA [auth A] Focus chain NB [auth F] Focus chain OA [auth A] Focus chain OB [auth F] Focus chain OE [auth W] Focus chain PE [auth W] Focus chain RC [auth N] Focus chain RD [auth P] Focus chain SC [auth N] Focus chain SD [auth P] Focus chain TA [auth B] Focus chain TB [auth G] Focus chain TC [auth N] Focus chain TD [auth P] Focus chain UA [auth B] Focus chain UC [auth N] Focus chain UD [auth P] Focus chain VC [auth N] Focus chain WC [auth N] Focus chain WD [auth P] Focus chain XC [auth N] Focus chain XE [auth Y] Focus chain YC [auth N] Focus chain ZC [auth N] Focus chain ZD [auth Q] Interactions & Density Focus chain AD [auth N] Focus chain BD [auth N] Focus chain BE [auth R] Focus chain CD [auth N] Focus chain DE [auth S] Focus chain EE [auth S] Focus chain FB [auth C] Focus chain FC [auth L] Focus chain FD [auth O] Focus chain FE [auth S] Focus chain GB [auth C] Focus chain GC [auth L] Focus chain GD [auth O] Focus chain GE [auth S] Focus chain HE [auth S] Focus chain IA [auth A] Focus chain IC [auth M] Focus chain IE [auth S] Focus chain JA [auth A] Focus chain KA [auth A] Focus chain LA [auth A] Focus chain LB [auth F] Focus chain MA [auth A] Focus chain MB [auth F] Focus chain NA [auth A] Focus chain NB [auth F] Focus chain OA [auth A] Focus chain OB [auth F] Focus chain OE [auth W] Focus chain PE [auth W] Focus chain RC [auth N] Focus chain RD [auth P] Focus chain SC [auth N] Focus chain SD [auth P] Focus chain TA [auth B] Focus chain TB [auth G] Focus chain TC [auth N] Focus chain TD [auth P] Focus chain UA [auth B] Focus chain UC [auth N] Focus chain UD [auth P] Focus chain VC [auth N] Focus chain WC [auth N] Focus chain WD [auth P] Focus chain XC [auth N] Focus chain XE [auth Y] Focus chain YC [auth N] Focus chain ZC [auth N] Focus chain ZD [auth Q]
PER Query on PER Download:Ideal Coordinates CCD File SDF format, chain FA [auth A] SDF format, chain OC [auth N] MOL2 format, chain FA [auth A] MOL2 format, chain OC [auth N] mmCIF format, chain FA [auth A] mmCIF format, chain OC [auth N]	FA [auth A], OC [auth N]	PEROXIDE ION O₂ ANAIPYUSIMHBEL-UHFFFAOYSA-N		Interactions Focus chain FA [auth A] Focus chain OC [auth N] Interactions & Density Focus chain FA [auth A] Focus chain OC [auth N]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain DA [auth A] SDF format, chain MC [auth N] MOL2 format, chain DA [auth A] MOL2 format, chain MC [auth N] mmCIF format, chain DA [auth A] mmCIF format, chain MC [auth N]	DA [auth A], MC [auth N]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain DA [auth A] Focus chain MC [auth N] Interactions & Density Focus chain DA [auth A] Focus chain MC [auth N]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain EA [auth A] SDF format, chain KD [auth P] SDF format, chain NC [auth N] SDF format, chain WA [auth C] MOL2 format, chain EA [auth A] MOL2 format, chain KD [auth P] MOL2 format, chain NC [auth N] MOL2 format, chain WA [auth C] mmCIF format, chain EA [auth A] mmCIF format, chain KD [auth P] mmCIF format, chain NC [auth N] mmCIF format, chain WA [auth C]	EA [auth A], KD [auth P], NC [auth N], WA [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain EA [auth A] Focus chain KD [auth P] Focus chain NC [auth N] Focus chain WA [auth C] Interactions & Density Focus chain EA [auth A] Focus chain KD [auth P] Focus chain NC [auth N] Focus chain WA [auth C]

Modified Residues 3 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
FME Query on FME	A, N	L-PEPTIDE LINKING	C₆ H₁₁ N O₃ S		MET
TPO Query on TPO	G, T	L-PEPTIDE LINKING	C₄ H₁₀ N O₆ P		THR
SAC Query on SAC	I, V	L-PEPTIDE LINKING	C₅ H₉ N O₄		SER

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.227 (Depositor), 0.227 (DCC)
R-Value Work: 0.185 (Depositor), 0.185 (DCC)
R-Value Observed: 0.188 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 182.6	α = 90
b = 204.51	β = 90
c = 178.29	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2022-07-20

Deposition Author(s):

Tsukihara, T.

Hirata, K.

Ago, H.

Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	18K06092

Revision History (Full details and data files)

Version 1.0: 2022-07-20
Type: Initial release
Version 1.1: 2023-11-29
Changes: Data collection, Refinement description
Version 1.2: 2024-05-01
Changes: Database references
Version 1.3: 2025-09-17
Changes: Advisory, Derived calculations, Structure summary

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.

7Y44 | pdb_00007y44

Re-refinement of damage free X-ray structure of bovine cytochrome c oxidase at 1.9 angstrom resolution

Literature

Determination of damage-free crystal structure of an X-ray-sensitive protein using an XFEL.

Biological Assembly 1

Biological Assembly 2

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Entity ID: 2

UniProt

Entity Groups

Sequence Annotations

Entity ID: 3

UniProt

Entity Groups

Sequence Annotations

Entity ID: 4

UniProt

Entity Groups

Sequence Annotations

Entity ID: 5

UniProt

Entity Groups

Sequence Annotations

Entity ID: 6

UniProt

Entity Groups

Sequence Annotations

Entity ID: 7

UniProt

Entity Groups

Sequence Annotations

Entity ID: 8

UniProt

Entity Groups

Sequence Annotations

Entity ID: 9

UniProt

Entity Groups

Sequence Annotations

Entity ID: 10

UniProt

Entity Groups

Sequence Annotations

Entity ID: 11

UniProt

Entity Groups

Sequence Annotations

Entity ID: 12

UniProt

Entity Groups

Sequence Annotations

Entity ID: 13

UniProt

Entity Groups

Sequence Annotations

Small Molecules

Experimental Data & Validation

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Entry History

Deposition Data

Revision History (Full details and data files)