9QR3 | pdb_00009qr3

Methyl-coenzyme M reductase of an ANME-2c from a microbial enrichment

PDB DOI: https://doi.org/10.2210/pdb9QR3/pdb

Classification: TRANSFERASE
Organism(s): Candidatus Methanogasteraceae archaeon
Mutation(s): No

Deposited: 2025-04-02 Released: 2025-07-16
Deposition Author(s): Mueller, M.-C., Wagner, T.
Funding Organization(s): European Research Council (ERC), German Research Foundation (DFG), Netherlands Organisation for Scientific Research (NWO), Max Planck Society

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.34 Å
R-Value Free:
0.147 (Depositor), 0.146 (DCC)
R-Value Work:
0.112 (Depositor), 0.114 (DCC)
R-Value Observed:
0.114 (Depositor)

Starting Model: in silico
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Atomic resolution structures of the methane-activating enzyme in anaerobic methanotrophy reveal extensive post-translational modifications.

Muller, M.C., Wissink, M., Mukherjee, P., Von Possel, N., Laso-Perez, R., Engilberge, S., Carpentier, P., Kahnt, J., Wegener, G., Welte, C.U., Wagner, T.

(2025) Nat Commun 16: 8229-8229

PubMed: 40913044 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41467-025-63387-1
Primary Citation Related Structures:
9QM5, 9QQT, 9QR1, 9QR3

PubMed Abstract:
Anaerobic methanotrophic archaea (ANME) are crucial to planetary carbon cycling. They oxidise methane in anoxic niches by transferring electrons to nitrate, metal oxides, or sulfate-reducing bacteria. No ANMEs have been isolated, hampering the biochemical investigation of anaerobic methane oxidation. Here, we obtained the true atomic resolution structure of their methane-capturing system (Methyl-Coenzyme M Reductase, MCR), circumventing the isolation barrier by exploiting microbial enrichments of freshwater nitrate-reducing ANME-2d grown in bioreactors, and marine ANME-2c in syntrophy with bacterial partners. Despite their physiological differences, these ANMEs have extremely conserved MCR structures, similar to homologs from methanogenic Methanosarcinales, rather than the phylogenetically distant MCR of ANME-1 isolated from Black Sea mats. The three studied enzymes have seven post-translational modifications, among them was a novel 3(S)-methylhistidine on the γ-chain of both ANME-2d MCRs. Labelling with gaseous krypton did not reveal any internal channels that would facilitate alkane diffusion to the active site, as observed in the ethane-specialised enzyme. Based on our data, the methanotrophic MCRs should follow the same radical reaction mechanism proposed for the methane-generating homologues. The described pattern of post-translational modifications underscores the importance of native purification as a powerful approach to discovering intrinsic enzymatic features in non-isolated microorganisms existing in nature.

Organizational Affiliation

Max-Planck-Institute for Marine Microbiology, Bremen, Germany.

Macromolecule Content

Total Structure Weight: 1,115.23 kDa
Atom Count: 88,317
Modeled Residue Count: 10,052
Deposited Residue Count: 10,080
Unique protein chains: 3

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha subunit of the Methyl-coenzyme M reductase from ANME-2c	A, D, G, J, M A, D, G, J, M, P, S, V	561	Candidatus Methanogasteraceae archaeon	Mutation(s): 0 EC: 2.8.4.1
UniProt
Find proteins for G7WN24 (Methanothrix harundinacea (strain 6Ac)) Explore G7WN24 Go to UniProtKB: G7WN24
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	G7WN24
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta subunit of the Methyl-coenzyme M reductase from ANME-2c	B, E, H, K, N B, E, H, K, N, Q, T, W	434	Candidatus Methanogasteraceae archaeon	Mutation(s): 0 EC: 2.8.4.1
UniProt
Find proteins for G7WN21 (Methanothrix harundinacea (strain 6Ac)) Explore G7WN21 Go to UniProtKB: G7WN21
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	G7WN21
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Gamma subunit of the Methyl-coenzyme M reductase from ANME-2c	C, F, I, L, O C, F, I, L, O, R, U, X	265	Candidatus Methanogasteraceae archaeon	Mutation(s): 0 EC: 2.8.4.1

Small Molecules

Ligands 9 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
F43 (Subject of Investigation/LOI) Query on F43 Download:Ideal Coordinates CCD File SDF format, chain CB [auth G] SDF format, chain ED [auth S] SDF format, chain IB [auth G] SDF format, chain KA [auth A] SDF format, chain ZC [auth S] SDF format, chain OC [auth P] SDF format, chain BC [auth M] SDF format, chain BA [auth A] MOL2 format, chain CB [auth G] MOL2 format, chain ED [auth S] MOL2 format, chain IB [auth G] MOL2 format, chain KA [auth A] MOL2 format, chain ZC [auth S] MOL2 format, chain OC [auth P] MOL2 format, chain BC [auth M] MOL2 format, chain BA [auth A] mmCIF format, chain CB [auth G] mmCIF format, chain ED [auth S] mmCIF format, chain IB [auth G] mmCIF format, chain KA [auth A] mmCIF format, chain ZC [auth S] mmCIF format, chain OC [auth P] mmCIF format, chain BC [auth M] mmCIF format, chain BA [auth A]	BA [auth A] BC [auth M] CB [auth G] ED [auth S] IB [auth G] BA [auth A], BC [auth M], CB [auth G], ED [auth S], IB [auth G], KA [auth A], OC [auth P], ZC [auth S]	FACTOR 430 C₄₂ H₅₁ N₆ Ni O₁₃ XLFIRMYGVLUNOY-SXMZNAGASA-M		Interactions Focus chain BA [auth A] Focus chain BC [auth M] Focus chain CB [auth G] Focus chain ED [auth S] Focus chain IB [auth G] Focus chain KA [auth A] Focus chain OC [auth P] Focus chain ZC [auth S] Interactions & Density Focus chain BA [auth A] Focus chain BC [auth M] Focus chain CB [auth G] Focus chain ED [auth S] Focus chain IB [auth G] Focus chain KA [auth A] Focus chain OC [auth P] Focus chain ZC [auth S]
TP7 (Subject of Investigation/LOI) Query on TP7 Download:Ideal Coordinates CCD File SDF format, chain BD [auth S] SDF format, chain DA [auth A] SDF format, chain NC [auth P] SDF format, chain OB [auth J] SDF format, chain QA [auth D] SDF format, chain JD [auth V] SDF format, chain EB [auth G] SDF format, chain DC [auth M] MOL2 format, chain BD [auth S] MOL2 format, chain DA [auth A] MOL2 format, chain NC [auth P] MOL2 format, chain OB [auth J] MOL2 format, chain QA [auth D] MOL2 format, chain JD [auth V] MOL2 format, chain EB [auth G] MOL2 format, chain DC [auth M] mmCIF format, chain BD [auth S] mmCIF format, chain DA [auth A] mmCIF format, chain NC [auth P] mmCIF format, chain OB [auth J] mmCIF format, chain QA [auth D] mmCIF format, chain JD [auth V] mmCIF format, chain EB [auth G] mmCIF format, chain DC [auth M]	BD [auth S] DA [auth A] DC [auth M] EB [auth G] JD [auth V] BD [auth S], DA [auth A], DC [auth M], EB [auth G], JD [auth V], NC [auth P], OB [auth J], QA [auth D]	Coenzyme B C₁₁ H₂₂ N O₇ P S JBJSVEVEEGOEBZ-SCZZXKLOSA-N		Interactions Focus chain BD [auth S] Focus chain DA [auth A] Focus chain DC [auth M] Focus chain EB [auth G] Focus chain JD [auth V] Focus chain NC [auth P] Focus chain OB [auth J] Focus chain QA [auth D] Interactions & Density Focus chain BD [auth S] Focus chain DA [auth A] Focus chain DC [auth M] Focus chain EB [auth G] Focus chain JD [auth V] Focus chain NC [auth P] Focus chain OB [auth J] Focus chain QA [auth D]
COM (Subject of Investigation/LOI) Query on COM Download:Ideal Coordinates CCD File SDF format, chain AD [auth S] SDF format, chain CA [auth A] SDF format, chain CC [auth M] SDF format, chain KD [auth V] SDF format, chain PB [auth J] SDF format, chain PC [auth P] SDF format, chain RA [auth D] SDF format, chain DB [auth G] MOL2 format, chain AD [auth S] MOL2 format, chain CA [auth A] MOL2 format, chain CC [auth M] MOL2 format, chain KD [auth V] MOL2 format, chain PB [auth J] MOL2 format, chain PC [auth P] MOL2 format, chain RA [auth D] MOL2 format, chain DB [auth G] mmCIF format, chain AD [auth S] mmCIF format, chain CA [auth A] mmCIF format, chain CC [auth M] mmCIF format, chain KD [auth V] mmCIF format, chain PB [auth J] mmCIF format, chain PC [auth P] mmCIF format, chain RA [auth D] mmCIF format, chain DB [auth G]	AD [auth S] CA [auth A] CC [auth M] DB [auth G] KD [auth V] AD [auth S], CA [auth A], CC [auth M], DB [auth G], KD [auth V], PB [auth J], PC [auth P], RA [auth D]	1-THIOETHANESULFONIC ACID C₂ H₆ O₃ S₂ ZNEWHQLOPFWXOF-UHFFFAOYSA-N		Interactions Focus chain AD [auth S] Focus chain CA [auth A] Focus chain CC [auth M] Focus chain DB [auth G] Focus chain KD [auth V] Focus chain PB [auth J] Focus chain PC [auth P] Focus chain RA [auth D] Interactions & Density Focus chain AD [auth S] Focus chain CA [auth A] Focus chain CC [auth M] Focus chain DB [auth G] Focus chain KD [auth V] Focus chain PB [auth J] Focus chain PC [auth P] Focus chain RA [auth D]
MPD Query on MPD Download:Ideal Coordinates CCD File SDF format, chain GA [auth A] SDF format, chain HC [auth N] SDF format, chain MD [auth V] SDF format, chain RC [auth P] SDF format, chain SB [auth J] SDF format, chain TA [auth D] SDF format, chain WB [auth K] SDF format, chain VB [auth K] SDF format, chain RB [auth J] SDF format, chain MA [auth B] SDF format, chain LB [auth H] MOL2 format, chain GA [auth A] MOL2 format, chain HC [auth N] MOL2 format, chain MD [auth V] MOL2 format, chain RC [auth P] MOL2 format, chain SB [auth J] MOL2 format, chain TA [auth D] MOL2 format, chain WB [auth K] MOL2 format, chain VB [auth K] MOL2 format, chain RB [auth J] MOL2 format, chain MA [auth B] MOL2 format, chain LB [auth H] mmCIF format, chain GA [auth A] mmCIF format, chain HC [auth N] mmCIF format, chain MD [auth V] mmCIF format, chain RC [auth P] mmCIF format, chain SB [auth J] mmCIF format, chain TA [auth D] mmCIF format, chain WB [auth K] mmCIF format, chain VB [auth K] mmCIF format, chain RB [auth J] mmCIF format, chain MA [auth B] mmCIF format, chain LB [auth H]	GA [auth A] HC [auth N] LB [auth H] MA [auth B] MD [auth V] GA [auth A], HC [auth N], LB [auth H], MA [auth B], MD [auth V], RB [auth J], RC [auth P], SB [auth J], TA [auth D], VB [auth K], WB [auth K]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain GA [auth A] Focus chain HC [auth N] Focus chain LB [auth H] Focus chain MA [auth B] Focus chain MD [auth V] Focus chain RB [auth J] Focus chain RC [auth P] Focus chain SB [auth J] Focus chain TA [auth D] Focus chain VB [auth K] Focus chain WB [auth K] Interactions & Density Focus chain GA [auth A] Focus chain HC [auth N] Focus chain LB [auth H] Focus chain MA [auth B] Focus chain MD [auth V] Focus chain RB [auth J] Focus chain RC [auth P] Focus chain SB [auth J] Focus chain TA [auth D] Focus chain VB [auth K] Focus chain WB [auth K]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain CD [auth S] SDF format, chain EA [auth A] SDF format, chain FB [auth G] SDF format, chain FC [auth M] SDF format, chain GB [auth G] SDF format, chain HA [auth A] SDF format, chain LD [auth V] SDF format, chain QB [auth J] SDF format, chain UA [auth D] SDF format, chain UC [auth Q] SDF format, chain WC [auth R] SDF format, chain YA [auth F] SDF format, chain YB [auth L] SDF format, chain SA [auth D] SDF format, chain QC [auth P] SDF format, chain KC [auth O] SDF format, chain FA [auth A] SDF format, chain EC [auth M] MOL2 format, chain CD [auth S] MOL2 format, chain EA [auth A] MOL2 format, chain FB [auth G] MOL2 format, chain FC [auth M] MOL2 format, chain GB [auth G] MOL2 format, chain HA [auth A] MOL2 format, chain LD [auth V] MOL2 format, chain QB [auth J] MOL2 format, chain UA [auth D] MOL2 format, chain UC [auth Q] MOL2 format, chain WC [auth R] MOL2 format, chain YA [auth F] MOL2 format, chain YB [auth L] MOL2 format, chain SA [auth D] MOL2 format, chain QC [auth P] MOL2 format, chain KC [auth O] MOL2 format, chain FA [auth A] MOL2 format, chain EC [auth M] mmCIF format, chain CD [auth S] mmCIF format, chain EA [auth A] mmCIF format, chain FB [auth G] mmCIF format, chain FC [auth M] mmCIF format, chain GB [auth G] mmCIF format, chain HA [auth A] mmCIF format, chain LD [auth V] mmCIF format, chain QB [auth J] mmCIF format, chain UA [auth D] mmCIF format, chain UC [auth Q] mmCIF format, chain WC [auth R] mmCIF format, chain YA [auth F] mmCIF format, chain YB [auth L] mmCIF format, chain SA [auth D] mmCIF format, chain QC [auth P] mmCIF format, chain KC [auth O] mmCIF format, chain FA [auth A] mmCIF format, chain EC [auth M]	CD [auth S] EA [auth A] EC [auth M] FA [auth A] FB [auth G] CD [auth S], EA [auth A], EC [auth M], FA [auth A], FB [auth G], FC [auth M], GB [auth G], HA [auth A], KC [auth O], LD [auth V], QB [auth J], QC [auth P], SA [auth D], UA [auth D], UC [auth Q], WC [auth R], YA [auth F], YB [auth L]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain CD [auth S] Focus chain EA [auth A] Focus chain EC [auth M] Focus chain FA [auth A] Focus chain FB [auth G] Focus chain FC [auth M] Focus chain GB [auth G] Focus chain HA [auth A] Focus chain KC [auth O] Focus chain LD [auth V] Focus chain QB [auth J] Focus chain QC [auth P] Focus chain SA [auth D] Focus chain UA [auth D] Focus chain UC [auth Q] Focus chain WC [auth R] Focus chain YA [auth F] Focus chain YB [auth L] Interactions & Density Focus chain CD [auth S] Focus chain EA [auth A] Focus chain EC [auth M] Focus chain FA [auth A] Focus chain FB [auth G] Focus chain FC [auth M] Focus chain GB [auth G] Focus chain HA [auth A] Focus chain KC [auth O] Focus chain LD [auth V] Focus chain QB [auth J] Focus chain QC [auth P] Focus chain SA [auth D] Focus chain UA [auth D] Focus chain UC [auth Q] Focus chain WC [auth R] Focus chain YA [auth F] Focus chain YB [auth L]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain DD [auth S] SDF format, chain HB [auth G] SDF format, chain IC [auth N] SDF format, chain JA [auth A] SDF format, chain ND [auth V] SDF format, chain SC [auth P] SDF format, chain ZA [auth F] SDF format, chain VA [auth D] SDF format, chain IA [auth A] MOL2 format, chain DD [auth S] MOL2 format, chain HB [auth G] MOL2 format, chain IC [auth N] MOL2 format, chain JA [auth A] MOL2 format, chain ND [auth V] MOL2 format, chain SC [auth P] MOL2 format, chain ZA [auth F] MOL2 format, chain VA [auth D] MOL2 format, chain IA [auth A] mmCIF format, chain DD [auth S] mmCIF format, chain HB [auth G] mmCIF format, chain IC [auth N] mmCIF format, chain JA [auth A] mmCIF format, chain ND [auth V] mmCIF format, chain SC [auth P] mmCIF format, chain ZA [auth F] mmCIF format, chain VA [auth D] mmCIF format, chain IA [auth A]	DD [auth S] HB [auth G] IA [auth A] IC [auth N] JA [auth A] DD [auth S], HB [auth G], IA [auth A], IC [auth N], JA [auth A], ND [auth V], SC [auth P], VA [auth D], ZA [auth F]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain DD [auth S] Focus chain HB [auth G] Focus chain IA [auth A] Focus chain IC [auth N] Focus chain JA [auth A] Focus chain ND [auth V] Focus chain SC [auth P] Focus chain VA [auth D] Focus chain ZA [auth F] Interactions & Density Focus chain DD [auth S] Focus chain HB [auth G] Focus chain IA [auth A] Focus chain IC [auth N] Focus chain JA [auth A] Focus chain ND [auth V] Focus chain SC [auth P] Focus chain VA [auth D] Focus chain ZA [auth F]
K Query on K Download:Ideal Coordinates CCD File SDF format, chain AB [auth G] SDF format, chain XC [auth S] SDF format, chain ZB [auth M] SDF format, chain Y [auth A] MOL2 format, chain AB [auth G] MOL2 format, chain XC [auth S] MOL2 format, chain ZB [auth M] MOL2 format, chain Y [auth A] mmCIF format, chain AB [auth G] mmCIF format, chain XC [auth S] mmCIF format, chain ZB [auth M] mmCIF format, chain Y [auth A]	AB [auth G], XC [auth S], Y [auth A], ZB [auth M]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain AB [auth G] Focus chain XC [auth S] Focus chain Y [auth A] Focus chain ZB [auth M] Interactions & Density Focus chain AB [auth G] Focus chain XC [auth S] Focus chain Y [auth A] Focus chain ZB [auth M]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain AA [auth A] SDF format, chain GC [auth N] SDF format, chain GD [auth U] SDF format, chain ID [auth V] SDF format, chain JC [auth O] SDF format, chain KB [auth H] SDF format, chain LA [auth B] SDF format, chain MB [auth I] SDF format, chain MC [auth P] SDF format, chain NA [auth C] SDF format, chain PA [auth D] SDF format, chain TB [auth K] SDF format, chain UB [auth K] SDF format, chain XA [auth F] SDF format, chain XB [auth L] SDF format, chain YC [auth S] SDF format, chain WA [auth E] SDF format, chain VC [auth R] SDF format, chain TC [auth Q] SDF format, chain PD [auth X] SDF format, chain OD [auth W] SDF format, chain NB [auth J] SDF format, chain FD [auth T] SDF format, chain BB [auth G] SDF format, chain AC [auth M] MOL2 format, chain AA [auth A] MOL2 format, chain GC [auth N] MOL2 format, chain GD [auth U] MOL2 format, chain ID [auth V] MOL2 format, chain JC [auth O] MOL2 format, chain KB [auth H] MOL2 format, chain LA [auth B] MOL2 format, chain MB [auth I] MOL2 format, chain MC [auth P] MOL2 format, chain NA [auth C] MOL2 format, chain PA [auth D] MOL2 format, chain TB [auth K] MOL2 format, chain UB [auth K] MOL2 format, chain XA [auth F] MOL2 format, chain XB [auth L] MOL2 format, chain YC [auth S] MOL2 format, chain WA [auth E] MOL2 format, chain VC [auth R] MOL2 format, chain TC [auth Q] MOL2 format, chain PD [auth X] MOL2 format, chain OD [auth W] MOL2 format, chain NB [auth J] MOL2 format, chain FD [auth T] MOL2 format, chain BB [auth G] MOL2 format, chain AC [auth M] mmCIF format, chain AA [auth A] mmCIF format, chain GC [auth N] mmCIF format, chain GD [auth U] mmCIF format, chain ID [auth V] mmCIF format, chain JC [auth O] mmCIF format, chain KB [auth H] mmCIF format, chain LA [auth B] mmCIF format, chain MB [auth I] mmCIF format, chain MC [auth P] mmCIF format, chain NA [auth C] mmCIF format, chain PA [auth D] mmCIF format, chain TB [auth K] mmCIF format, chain UB [auth K] mmCIF format, chain XA [auth F] mmCIF format, chain XB [auth L] mmCIF format, chain YC [auth S] mmCIF format, chain WA [auth E] mmCIF format, chain VC [auth R] mmCIF format, chain TC [auth Q] mmCIF format, chain PD [auth X] mmCIF format, chain OD [auth W] mmCIF format, chain NB [auth J] mmCIF format, chain FD [auth T] mmCIF format, chain BB [auth G] mmCIF format, chain AC [auth M]	AA [auth A] AC [auth M] BB [auth G] FD [auth T] GC [auth N] AA [auth A], AC [auth M], BB [auth G], FD [auth T], GC [auth N], GD [auth U], ID [auth V], JC [auth O], KB [auth H], LA [auth B], MB [auth I], MC [auth P], NA [auth C], NB [auth J], OD [auth W], PA [auth D], PD [auth X], TB [auth K], TC [auth Q], UB [auth K], VC [auth R], WA [auth E], XA [auth F], XB [auth L], YC [auth S]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain AA [auth A] Focus chain AC [auth M] Focus chain BB [auth G] Focus chain FD [auth T] Focus chain GC [auth N] Focus chain GD [auth U] Focus chain ID [auth V] Focus chain JC [auth O] Focus chain KB [auth H] Focus chain LA [auth B] Focus chain MB [auth I] Focus chain MC [auth P] Focus chain NA [auth C] Focus chain NB [auth J] Focus chain OD [auth W] Focus chain PA [auth D] Focus chain PD [auth X] Focus chain TB [auth K] Focus chain TC [auth Q] Focus chain UB [auth K] Focus chain VC [auth R] Focus chain WA [auth E] Focus chain XA [auth F] Focus chain XB [auth L] Focus chain YC [auth S] Interactions & Density Focus chain AA [auth A] Focus chain AC [auth M] Focus chain BB [auth G] Focus chain FD [auth T] Focus chain GC [auth N] Focus chain GD [auth U] Focus chain ID [auth V] Focus chain JC [auth O] Focus chain KB [auth H] Focus chain LA [auth B] Focus chain MB [auth I] Focus chain MC [auth P] Focus chain NA [auth C] Focus chain NB [auth J] Focus chain OD [auth W] Focus chain PA [auth D] Focus chain PD [auth X] Focus chain TB [auth K] Focus chain TC [auth Q] Focus chain UB [auth K] Focus chain VC [auth R] Focus chain WA [auth E] Focus chain XA [auth F] Focus chain XB [auth L] Focus chain YC [auth S]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain HD [auth V] SDF format, chain JB [auth H] SDF format, chain OA [auth D] SDF format, chain Z [auth A] SDF format, chain LC [auth P] MOL2 format, chain HD [auth V] MOL2 format, chain JB [auth H] MOL2 format, chain OA [auth D] MOL2 format, chain Z [auth A] MOL2 format, chain LC [auth P] mmCIF format, chain HD [auth V] mmCIF format, chain JB [auth H] mmCIF format, chain OA [auth D] mmCIF format, chain Z [auth A] mmCIF format, chain LC [auth P]	HD [auth V], JB [auth H], LC [auth P], OA [auth D], Z [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain HD [auth V] Focus chain JB [auth H] Focus chain LC [auth P] Focus chain OA [auth D] Focus chain Z [auth A] Interactions & Density Focus chain HD [auth V] Focus chain JB [auth H] Focus chain LC [auth P] Focus chain OA [auth D] Focus chain Z [auth A]

Modified Residues 7 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
AGM Query on AGM	A, D, G, J, M A, D, G, J, M, P, S, V	L-PEPTIDE LINKING	C₇ H₁₇ N₄ O₂		ARG
DYA Query on DYA	A, D, G, J, M A, D, G, J, M, P, S, V	L-PEPTIDE LINKING	C₄ H₅ N O₄		ASP
GL3 Query on GL3	A, D, G, J, M A, D, G, J, M, P, S, V	L-PEPTIDE LINKING	C₂ H₅ N O S		GLY
MGN Query on MGN	A, D, G, J, M A, D, G, J, M, P, S, V	L-PEPTIDE LINKING	C₆ H₁₂ N₂ O₃		GLN
MHS Query on MHS	A, D, G, J, M A, D, G, J, M, P, S, V	L-PEPTIDE LINKING	C₇ H₁₁ N₃ O₂		HIS
SMC Query on SMC	A, D, G, J, M A, D, G, J, M, P, S, V	L-PEPTIDE LINKING	C₄ H₉ N O₂ S		CYS
TRX Query on TRX	A, D, G, J, M A, D, G, J, M, P, S, V	L-PEPTIDE LINKING	C₁₁ H₁₂ N₂ O₃		TRP

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.34 Å
R-Value Free: 0.147 (Depositor), 0.146 (DCC)
R-Value Work: 0.112 (Depositor), 0.114 (DCC)
R-Value Observed: 0.114 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 156.867	α = 90
b = 157.456	β = 90.34
c = 215.422	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
autoPROC	data reduction
STARANISO	data scaling
PHASER	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: 2025-07-16

Deposition Author(s):

Mueller, M.-C.

Wagner, T.

Funding Organization	Location	Grant Number
European Research Council (ERC)	European Union	101125699
German Research Foundation (DFG)	Germany	WA 4053/1-1
Netherlands Organisation for Scientific Research (NWO)	Netherlands	VI.Vidi.223.012
Netherlands Organisation for Scientific Research (NWO)	Netherlands	024.002.002
Max Planck Society	Germany	--