SMTL ID : 7suc.1

XFEL Serial Crystallography Reveals the Room Temperature Structure of Methyl-Coenzyme M Reductase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

hetero-2-2-2-mer

Ligands

7 x MG: MAGNESIUM ION(Non-functional Binders)(Non-covalent)

MG.1: 1 residues within 4Å: Ligands: ACT.5 No protein-ligand interaction detected (PLIP) MG.7: 2 residues within 4Å: Chain B: Y.10, N.249 No protein-ligand interaction detected (PLIP) MG.8: 3 residues within 4Å: Chain C: K.26, E.29, K.134 3 PLIP interactions: 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.29, H2O.13, H2O.14 MG.9: 2 residues within 4Å: Chain D: E.375 Chain F: R.224 No protein-ligand interaction detected (PLIP) MG.10: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.14: 1 residues within 4Å: Chain E: K.291 No protein-ligand interaction detected (PLIP) MG.15: 2 residues within 4Å: Chain F: E.29, K.134 4 PLIP interactions: 1 interactions with chain F, 3 Ligand-Water interactions Metal complexes: F:E.29, H2O.28, H2O.29, H2O.29

2 x F43: FACTOR 430(Non-covalent)

F43.2: 41 residues within 4Å: Chain A: A.143, V.144, V.145, Q.146, M.149, V.150, M.228, Q.229, M.232, I.235, A.242, G.243 Chain D: G.325, G.326, V.327, G.328, F.329, T.330, Q.331, Y.332, F.395, G.396, G.397, S.398, Q.399, G.441, F.442 Chain E: S.364, I.365, Y.366 Chain F: L.116, S.117, G.118, R.119, K.152, S.153, V.154, H.155, G.156, H.157 Ligands: COM.12 38 PLIP interactions: 13 interactions with chain F, 14 interactions with chain D, 8 interactions with chain A, 3 interactions with chain E, Hydrophobic interactions: F:L.116, D:V.327, D:F.329, D:Y.332, D:Y.332, D:F.395, D:F.442, A:Q.146, A:I.235 Hydrogen bonds: F:S.117, F:S.117, F:G.118, F:S.153, F:V.154, F:G.156, D:V.327, D:G.328, D:Q.331, D:Q.331, D:Y.332, A:V.144, A:V.145, A:Q.146, A:Q.229, E:I.365, E:Y.366, E:Y.366 Water bridges: F:H.155, F:H.157, F:H.157, F:H.157, D:T.330, D:G.397, D:S.398, A:Q.146, A:E.147 Salt bridges: F:H.155, F:H.157 F43.11: 42 residues within 4Å: Chain A: G.325, G.326, V.327, G.328, F.329, T.330, Q.331, Y.332, F.395, G.396, G.397, S.398, Q.399, G.441, F.442, Y.443 Chain B: S.364, I.365, Y.366 Chain C: L.116, S.117, G.118, R.119, K.152, S.153, V.154, H.155, G.156, H.157 Chain D: A.143, V.144, V.145, Q.146, M.149, V.150, M.228, Q.229, M.232, I.235, A.242, G.243 Ligands: COM.4 37 PLIP interactions: 3 interactions with chain B, 7 interactions with chain D, 14 interactions with chain C, 13 interactions with chain A, Hydrogen bonds: B:I.365, B:Y.366, B:Y.366, D:V.144, D:V.145, D:Q.146, D:Q.229, C:S.117, C:S.117, C:G.118, C:R.119, C:S.153, C:V.154, A:V.327, A:G.328, A:Q.331, A:Q.331, A:Y.332 Hydrophobic interactions: D:Q.146, D:I.235, C:L.116, A:V.327, A:F.329, A:Y.332, A:Y.332, A:F.395, A:F.442 Water bridges: D:Q.146, C:S.117, C:H.155, C:G.156, C:G.156, C:H.157, A:T.330, A:G.397 Salt bridges: C:H.155, C:H.157

2 x TP7: Coenzyme B

TP7.3: 21 residues within 4Å: Chain A: R.269, R.270, L.319, M.323, S.324, F.329, F.442, M.479, N.480, V.481 Chain B: F.360, F.361, Y.366, G.367, G.368, H.378, I.379, V.380 Chain D: R.224, K.255, H.256 19 PLIP interactions: 6 interactions with chain D, 9 interactions with chain B, 4 interactions with chain A Hydrogen bonds: D:K.255, B:G.368 Water bridges: D:R.224, D:R.224, B:Y.366, B:H.378, A:R.269, A:M.323 Salt bridges: D:R.224, D:K.255, D:K.255, B:H.378, A:R.269 Hydrophobic interactions: B:F.361, B:F.361, B:Y.366, B:I.379, B:V.380, A:F.329 TP7.6: 21 residues within 4Å: Chain A: R.224, K.255, H.256 Chain D: R.269, R.270, L.319, M.323, S.324, F.329, F.442, M.479, N.480, V.481 Chain E: F.360, F.361, Y.366, G.367, G.368, H.378, I.379, V.380 20 PLIP interactions: 6 interactions with chain A, 9 interactions with chain E, 5 interactions with chain D Hydrogen bonds: A:K.255, E:G.368 Water bridges: A:R.224, A:R.224, E:Y.366, E:H.378, D:R.269, D:M.323 Salt bridges: A:R.224, A:K.255, A:K.255, E:H.378, D:R.269 Hydrophobic interactions: E:F.361, E:F.361, E:Y.366, E:I.379, E:V.380, D:M.323, D:F.329

2 x COM: 1-THIOETHANESULFONIC ACID(Non-covalent)

COM.4: 9 residues within 4Å: Chain A: Y.332, F.442, Y.443 Chain B: F.360, S.364, Y.366 Chain C: L.116, R.119 Ligands: F43.11 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain C Hydrogen bonds: A:Y.443 Water bridges: C:R.119, C:R.119 Salt bridges: C:R.119 COM.12: 9 residues within 4Å: Chain D: Y.332, F.442, Y.443 Chain E: F.360, S.364, Y.366 Chain F: L.116, R.119 Ligands: F43.2 4 PLIP interactions: 3 interactions with chain F, 1 interactions with chain D Water bridges: F:R.119, F:R.119 Salt bridges: F:R.119 Hydrogen bonds: D:Y.443

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.5: 6 residues within 4Å: Chain A: V.518, K.530, E.535, F.536, E.537 Ligands: MG.1 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.536 Hydrogen bonds: A:E.537 Water bridges: A:V.518, A:K.530 Salt bridges: A:K.530

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.13: 2 residues within 4Å: Chain D: L.4, Y.347 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ohmer, C.J. et al., XFEL serial crystallography reveals the room temperature structure of methyl-coenzyme M reductase. J.Inorg.Biochem. (2022)

Release Date

2022-03-02

Peptides

Methyl-coenzyme M reductase I subunit alpha: AD
Methyl-coenzyme M reductase I subunit beta: BE
Methyl-coenzyme M reductase I subunit gamma: CF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
a

B
B

E
b

C
C

F
c

Methyl-coenzyme M reductase I subunit alpha

Methyl-coenzyme M reductase I subunit beta

Methyl-coenzyme M reductase I subunit gamma

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