9OVF | pdb_00009ovf

Rubredoxin covalently linked to benzo-18-crown-6

PDB DOI: https://doi.org/10.2210/pdb9OVF/pdb

Classification: METAL BINDING PROTEIN
Organism(s): Desulfovibrio desulfuricans ATCC 27774
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2025-05-29 Released: 2025-12-03
Deposition Author(s): Adhami, N., Sawaya, M.R., Shafaat, H.S., Rodriguez, J.A., Spokoyny, A.M.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.45 Å
R-Value Free:
0.212 (Depositor), 0.200 (DCC)
R-Value Work:
0.199 (Depositor)
R-Value Observed:
0.200 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Site-selective Au(III)-mediated metalloenzyme conjugations

Adhami, N., Rebelo, M.J.P., Teptarkulkarn, H., Ando, S.H., Olivares, E.J., Goff, T.L., Munoz, A.J., Qu, S., Kerr, T.A., Coutinho, R.J., Sawaya, M.R., Shafaat, H.S., Rodrigues, J.A., Spokoyny, M.A.

To be published.

Macromolecule Content

Total Structure Weight: 60.2 kDa
Atom Count: 4,216
Modeled Residue Count: 449
Deposited Residue Count: 450
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Rubredoxin-1	A, B, C, D, E A, B, C, D, E, F, G, H, I, J	45	Desulfovibrio desulfuricans ATCC 27774	Mutation(s): 0 Gene Names: rd1, Ddes_2011
UniProt
Find proteins for P04170 (Desulfovibrio desulfuricans (strain ATCC 27774 / DSM 6949 / MB)) Explore P04170 Go to UniProtKB: P04170
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P04170
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
15P Query on 15P Download:Ideal Coordinates CCD File SDF format, chain QA [auth E] SDF format, chain W [auth B] MOL2 format, chain QA [auth E] MOL2 format, chain W [auth B] mmCIF format, chain QA [auth E] mmCIF format, chain W [auth B]	QA [auth E], W [auth B]	POLYETHYLENE GLYCOL (N=34) C₆₉ H₁₄₀ O₃₅ VUYXVWGKCKTUMF-UHFFFAOYSA-N		Interactions Focus chain QA [auth E] Focus chain W [auth B] Interactions & Density Focus chain QA [auth E] Focus chain W [auth B]
A1CET (Subject of Investigation/LOI) Query on A1CET Download:Ideal Coordinates CCD File SDF format, chain BA [auth C] SDF format, chain CB [auth F] SDF format, chain IC [auth J] SDF format, chain JA [auth D] SDF format, chain L [auth A] SDF format, chain LB [auth G] SDF format, chain SA [auth E] SDF format, chain SB [auth H] SDF format, chain U [auth B] SDF format, chain ZB [auth I] MOL2 format, chain BA [auth C] MOL2 format, chain CB [auth F] MOL2 format, chain IC [auth J] MOL2 format, chain JA [auth D] MOL2 format, chain L [auth A] MOL2 format, chain LB [auth G] MOL2 format, chain SA [auth E] MOL2 format, chain SB [auth H] MOL2 format, chain U [auth B] MOL2 format, chain ZB [auth I] mmCIF format, chain BA [auth C] mmCIF format, chain CB [auth F] mmCIF format, chain IC [auth J] mmCIF format, chain JA [auth D] mmCIF format, chain L [auth A] mmCIF format, chain LB [auth G] mmCIF format, chain SA [auth E] mmCIF format, chain SB [auth H] mmCIF format, chain U [auth B] mmCIF format, chain ZB [auth I]	BA [auth C] CB [auth F] IC [auth J] JA [auth D] L [auth A] BA [auth C], CB [auth F], IC [auth J], JA [auth D], L [auth A], LB [auth G], SA [auth E], SB [auth H], U [auth B], ZB [auth I]	2,3,5,6,8,9,11,12,14,15-decahydro-1,4,7,10,13,16-benzohexaoxacyclooctadecine-18-thiol C₁₆ H₂₄ O₆ S BPELBPJWXAPBFN-UHFFFAOYSA-N		Interactions Focus chain BA [auth C] Focus chain CB [auth F] Focus chain IC [auth J] Focus chain JA [auth D] Focus chain L [auth A] Focus chain LB [auth G] Focus chain SA [auth E] Focus chain SB [auth H] Focus chain U [auth B] Focus chain ZB [auth I] Interactions & Density Focus chain BA [auth C] Focus chain CB [auth F] Focus chain IC [auth J] Focus chain JA [auth D] Focus chain L [auth A] Focus chain LB [auth G] Focus chain SA [auth E] Focus chain SB [auth H] Focus chain U [auth B] Focus chain ZB [auth I]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain AC [auth I] SDF format, chain CA [auth C] SDF format, chain DB [auth F] SDF format, chain EA [auth C] SDF format, chain GC [auth J] SDF format, chain JB [auth G] SDF format, chain JC [auth J] SDF format, chain KA [auth D] SDF format, chain MA [auth D] SDF format, chain MB [auth G] SDF format, chain N [auth A] SDF format, chain TA [auth E] SDF format, chain V [auth B] SDF format, chain XB [auth I] SDF format, chain VA [auth E] SDF format, chain TB [auth H] SDF format, chain M [auth A] SDF format, chain AB [auth F] MOL2 format, chain AC [auth I] MOL2 format, chain CA [auth C] MOL2 format, chain DB [auth F] MOL2 format, chain EA [auth C] MOL2 format, chain GC [auth J] MOL2 format, chain JB [auth G] MOL2 format, chain JC [auth J] MOL2 format, chain KA [auth D] MOL2 format, chain MA [auth D] MOL2 format, chain MB [auth G] MOL2 format, chain N [auth A] MOL2 format, chain TA [auth E] MOL2 format, chain V [auth B] MOL2 format, chain XB [auth I] MOL2 format, chain VA [auth E] MOL2 format, chain TB [auth H] MOL2 format, chain M [auth A] MOL2 format, chain AB [auth F] mmCIF format, chain AC [auth I] mmCIF format, chain CA [auth C] mmCIF format, chain DB [auth F] mmCIF format, chain EA [auth C] mmCIF format, chain GC [auth J] mmCIF format, chain JB [auth G] mmCIF format, chain JC [auth J] mmCIF format, chain KA [auth D] mmCIF format, chain MA [auth D] mmCIF format, chain MB [auth G] mmCIF format, chain N [auth A] mmCIF format, chain TA [auth E] mmCIF format, chain V [auth B] mmCIF format, chain XB [auth I] mmCIF format, chain VA [auth E] mmCIF format, chain TB [auth H] mmCIF format, chain M [auth A] mmCIF format, chain AB [auth F]	AB [auth F] AC [auth I] CA [auth C] DB [auth F] EA [auth C] AB [auth F], AC [auth I], CA [auth C], DB [auth F], EA [auth C], GC [auth J], JB [auth G], JC [auth J], KA [auth D], M [auth A], MA [auth D], MB [auth G], N [auth A], TA [auth E], TB [auth H], V [auth B], VA [auth E], XB [auth I]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain AB [auth F] Focus chain AC [auth I] Focus chain CA [auth C] Focus chain DB [auth F] Focus chain EA [auth C] Focus chain GC [auth J] Focus chain JB [auth G] Focus chain JC [auth J] Focus chain KA [auth D] Focus chain M [auth A] Focus chain MA [auth D] Focus chain MB [auth G] Focus chain N [auth A] Focus chain TA [auth E] Focus chain TB [auth H] Focus chain V [auth B] Focus chain VA [auth E] Focus chain XB [auth I] Interactions & Density Focus chain AB [auth F] Focus chain AC [auth I] Focus chain CA [auth C] Focus chain DB [auth F] Focus chain EA [auth C] Focus chain GC [auth J] Focus chain JB [auth G] Focus chain JC [auth J] Focus chain KA [auth D] Focus chain M [auth A] Focus chain MA [auth D] Focus chain MB [auth G] Focus chain N [auth A] Focus chain TA [auth E] Focus chain TB [auth H] Focus chain V [auth B] Focus chain VA [auth E] Focus chain XB [auth I]
FE Query on FE Download:Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain BB [auth F] SDF format, chain HC [auth J] SDF format, chain IA [auth D] SDF format, chain KB [auth G] SDF format, chain RA [auth E] SDF format, chain RB [auth H] SDF format, chain T [auth B] SDF format, chain YB [auth I] SDF format, chain K [auth A] MOL2 format, chain AA [auth C] MOL2 format, chain BB [auth F] MOL2 format, chain HC [auth J] MOL2 format, chain IA [auth D] MOL2 format, chain KB [auth G] MOL2 format, chain RA [auth E] MOL2 format, chain RB [auth H] MOL2 format, chain T [auth B] MOL2 format, chain YB [auth I] MOL2 format, chain K [auth A] mmCIF format, chain AA [auth C] mmCIF format, chain BB [auth F] mmCIF format, chain HC [auth J] mmCIF format, chain IA [auth D] mmCIF format, chain KB [auth G] mmCIF format, chain RA [auth E] mmCIF format, chain RB [auth H] mmCIF format, chain T [auth B] mmCIF format, chain YB [auth I] mmCIF format, chain K [auth A]	AA [auth C] BB [auth F] HC [auth J] IA [auth D] K [auth A] AA [auth C], BB [auth F], HC [auth J], IA [auth D], K [auth A], KB [auth G], RA [auth E], RB [auth H], T [auth B], YB [auth I]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain BB [auth F] Focus chain HC [auth J] Focus chain IA [auth D] Focus chain K [auth A] Focus chain KB [auth G] Focus chain RA [auth E] Focus chain RB [auth H] Focus chain T [auth B] Focus chain YB [auth I] Interactions & Density Focus chain AA [auth C] Focus chain BB [auth F] Focus chain HC [auth J] Focus chain IA [auth D] Focus chain K [auth A] Focus chain KB [auth G] Focus chain RA [auth E] Focus chain RB [auth H] Focus chain T [auth B] Focus chain YB [auth I]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain BC [auth I] SDF format, chain CC [auth I] SDF format, chain DA [auth C] SDF format, chain DC [auth I] SDF format, chain EB [auth F] SDF format, chain EC [auth I] SDF format, chain FA [auth C] SDF format, chain FB [auth F] SDF format, chain FC [auth J] SDF format, chain GA [auth C] SDF format, chain GB [auth F] SDF format, chain HA [auth C] SDF format, chain HB [auth F] SDF format, chain IB [auth G] SDF format, chain KC [auth J] SDF format, chain LA [auth D] SDF format, chain NA [auth D] SDF format, chain NB [auth G] SDF format, chain OA [auth D] SDF format, chain OB [auth G] SDF format, chain P [auth A] SDF format, chain PA [auth D] SDF format, chain PB [auth G] SDF format, chain Q [auth A] SDF format, chain R [auth A] SDF format, chain S [auth A] SDF format, chain UA [auth E] SDF format, chain UB [auth H] SDF format, chain VB [auth H] SDF format, chain WA [auth E] SDF format, chain WB [auth I] SDF format, chain X [auth B] SDF format, chain XA [auth E] SDF format, chain Y [auth B] SDF format, chain YA [auth E] SDF format, chain Z [auth B] SDF format, chain ZA [auth F] SDF format, chain QB [auth H] SDF format, chain O [auth A] MOL2 format, chain BC [auth I] MOL2 format, chain CC [auth I] MOL2 format, chain DA [auth C] MOL2 format, chain DC [auth I] MOL2 format, chain EB [auth F] MOL2 format, chain EC [auth I] MOL2 format, chain FA [auth C] MOL2 format, chain FB [auth F] MOL2 format, chain FC [auth J] MOL2 format, chain GA [auth C] MOL2 format, chain GB [auth F] MOL2 format, chain HA [auth C] MOL2 format, chain HB [auth F] MOL2 format, chain IB [auth G] MOL2 format, chain KC [auth J] MOL2 format, chain LA [auth D] MOL2 format, chain NA [auth D] MOL2 format, chain NB [auth G] MOL2 format, chain OA [auth D] MOL2 format, chain OB [auth G] MOL2 format, chain P [auth A] MOL2 format, chain PA [auth D] MOL2 format, chain PB [auth G] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain S [auth A] MOL2 format, chain UA [auth E] MOL2 format, chain UB [auth H] MOL2 format, chain VB [auth H] MOL2 format, chain WA [auth E] MOL2 format, chain WB [auth I] MOL2 format, chain X [auth B] MOL2 format, chain XA [auth E] MOL2 format, chain Y [auth B] MOL2 format, chain YA [auth E] MOL2 format, chain Z [auth B] MOL2 format, chain ZA [auth F] MOL2 format, chain QB [auth H] MOL2 format, chain O [auth A] mmCIF format, chain BC [auth I] mmCIF format, chain CC [auth I] mmCIF format, chain DA [auth C] mmCIF format, chain DC [auth I] mmCIF format, chain EB [auth F] mmCIF format, chain EC [auth I] mmCIF format, chain FA [auth C] mmCIF format, chain FB [auth F] mmCIF format, chain FC [auth J] mmCIF format, chain GA [auth C] mmCIF format, chain GB [auth F] mmCIF format, chain HA [auth C] mmCIF format, chain HB [auth F] mmCIF format, chain IB [auth G] mmCIF format, chain KC [auth J] mmCIF format, chain LA [auth D] mmCIF format, chain NA [auth D] mmCIF format, chain NB [auth G] mmCIF format, chain OA [auth D] mmCIF format, chain OB [auth G] mmCIF format, chain P [auth A] mmCIF format, chain PA [auth D] mmCIF format, chain PB [auth G] mmCIF format, chain Q [auth A] mmCIF format, chain R [auth A] mmCIF format, chain S [auth A] mmCIF format, chain UA [auth E] mmCIF format, chain UB [auth H] mmCIF format, chain VB [auth H] mmCIF format, chain WA [auth E] mmCIF format, chain WB [auth I] mmCIF format, chain X [auth B] mmCIF format, chain XA [auth E] mmCIF format, chain Y [auth B] mmCIF format, chain YA [auth E] mmCIF format, chain Z [auth B] mmCIF format, chain ZA [auth F] mmCIF format, chain QB [auth H] mmCIF format, chain O [auth A]	BC [auth I] CC [auth I] DA [auth C] DC [auth I] EB [auth F] BC [auth I], CC [auth I], DA [auth C], DC [auth I], EB [auth F], EC [auth I], FA [auth C], FB [auth F], FC [auth J], GA [auth C], GB [auth F], HA [auth C], HB [auth F], IB [auth G], KC [auth J], LA [auth D], NA [auth D], NB [auth G], O [auth A], OA [auth D], OB [auth G], P [auth A], PA [auth D], PB [auth G], Q [auth A], QB [auth H], R [auth A], S [auth A], UA [auth E], UB [auth H], VB [auth H], WA [auth E], WB [auth I], X [auth B], XA [auth E], Y [auth B], YA [auth E], Z [auth B], ZA [auth F]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain BC [auth I] Focus chain CC [auth I] Focus chain DA [auth C] Focus chain DC [auth I] Focus chain EB [auth F] Focus chain EC [auth I] Focus chain FA [auth C] Focus chain FB [auth F] Focus chain FC [auth J] Focus chain GA [auth C] Focus chain GB [auth F] Focus chain HA [auth C] Focus chain HB [auth F] Focus chain IB [auth G] Focus chain KC [auth J] Focus chain LA [auth D] Focus chain NA [auth D] Focus chain NB [auth G] Focus chain O [auth A] Focus chain OA [auth D] Focus chain OB [auth G] Focus chain P [auth A] Focus chain PA [auth D] Focus chain PB [auth G] Focus chain Q [auth A] Focus chain QB [auth H] Focus chain R [auth A] Focus chain S [auth A] Focus chain UA [auth E] Focus chain UB [auth H] Focus chain VB [auth H] Focus chain WA [auth E] Focus chain WB [auth I] Focus chain X [auth B] Focus chain XA [auth E] Focus chain Y [auth B] Focus chain YA [auth E] Focus chain Z [auth B] Focus chain ZA [auth F] Interactions & Density Focus chain BC [auth I] Focus chain CC [auth I] Focus chain DA [auth C] Focus chain DC [auth I] Focus chain EB [auth F] Focus chain EC [auth I] Focus chain FA [auth C] Focus chain FB [auth F] Focus chain FC [auth J] Focus chain GA [auth C] Focus chain GB [auth F] Focus chain HA [auth C] Focus chain HB [auth F] Focus chain IB [auth G] Focus chain KC [auth J] Focus chain LA [auth D] Focus chain NA [auth D] Focus chain NB [auth G] Focus chain O [auth A] Focus chain OA [auth D] Focus chain OB [auth G] Focus chain P [auth A] Focus chain PA [auth D] Focus chain PB [auth G] Focus chain Q [auth A] Focus chain QB [auth H] Focus chain R [auth A] Focus chain S [auth A] Focus chain UA [auth E] Focus chain UB [auth H] Focus chain VB [auth H] Focus chain WA [auth E] Focus chain WB [auth I] Focus chain X [auth B] Focus chain XA [auth E] Focus chain Y [auth B] Focus chain YA [auth E] Focus chain Z [auth B] Focus chain ZA [auth F]