SMTL ID : 7sxm.1

Structure of Xenon-derivatized Methyl-Coenzyme M Reductase from Methanothermobacter marburgensis

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

hetero-2-2-2-mer

Ligands

2 x F43: FACTOR 430(Non-covalent)

F43.1: 34 residues within 4Å: Chain A: A.143, V.144, V.145, Q.146, M.149, M.228, Q.229, M.232, A.242 Chain D: G.325, G.326, V.327, G.328, F.329, T.330, Q.331, Y.332, F.395, G.396, 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, H.157 Ligands: COM.15 34 PLIP interactions: 14 interactions with chain D, 11 interactions with chain F, 6 interactions with chain A, 3 interactions with chain E, Hydrophobic interactions: D:V.327, D:F.329, D:Y.332, D:Y.332, D:F.395, D:F.442, F:L.116, A:Q.146 Hydrogen bonds: D:V.327, D:G.328, D:Q.331, D:Q.331, D:Y.332, D:Y.332, F:S.117, F:G.118, F:S.153, F:V.154, A:V.144, A:V.145, A:Q.146, A:Q.229, E:I.365, E:Y.366, E:Y.366 Water bridges: D:T.330, D:S.398, F:H.155, F:G.156, F:H.157, F:H.157, A:A.242 Salt bridges: F:H.155, F:H.157 F43.8: 35 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.441, F.442 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, H.157 Chain D: A.143, V.144, V.145, Q.146, M.149, M.228, Q.229, M.232, I.235, A.242 Ligands: COM.5 36 PLIP interactions: 14 interactions with chain C, 13 interactions with chain A, 2 interactions with chain B, 7 interactions with chain D, Hydrophobic interactions: C:L.116, A:V.327, A:F.329, A:Y.332, A:Y.332, A:F.395, A:F.442, D:Q.146, D:I.235 Hydrogen bonds: C:S.117, C:G.118, C:R.119, C:S.153, C:V.154, A:V.327, A:G.328, A:T.330, A:Q.331, A:Q.331, A:Y.332, B:I.365, B:Y.366, D:V.144, D:V.145, D:Q.146, D:Q.229 Water bridges: C:S.117, C:H.155, C:H.155, C:G.156, C:H.157, C:H.157, A:S.398, D:Q.146 Salt bridges: C:H.155, C:H.157

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: K.530 Ligands: ACT.3 5 PLIP interactions: 4 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: H2O.1, H2O.2, H2O.4, H2O.8, ACT.3 MG.17: 2 residues within 4Å: Chain D: K.530 Ligands: ACT.18 No protein-ligand interaction detected (PLIP)

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

ACT.3: 6 residues within 4Å: Chain A: V.518, K.530, E.535, F.536, E.537 Ligands: MG.2 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.536 Hydrogen bonds: A:E.537 Salt bridges: A:K.530 ACT.6: 8 residues within 4Å: Chain A: K.255 Chain E: F.361, Y.366, G.367, G.368, H.378, V.380 Ligands: TP7.9 4 PLIP interactions: 3 interactions with chain E, 1 interactions with chain A Hydrophobic interactions: E:F.361, E:V.380 Hydrogen bonds: E:G.368 Salt bridges: A:K.255 ACT.14: 8 residues within 4Å: Chain B: F.361, Y.366, G.367, G.368, H.378, V.380 Chain D: K.255 Ligands: TP7.4 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain D Hydrophobic interactions: B:F.361, B:V.380 Hydrogen bonds: B:G.368 Water bridges: D:K.255 Salt bridges: D:K.255 ACT.18: 6 residues within 4Å: Chain D: V.518, K.530, E.535, F.536, E.537 Ligands: MG.17 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:F.536 Hydrogen bonds: D:E.537 Water bridges: D:K.530, D:K.530 Salt bridges: D:K.530

2 x TP7: Coenzyme B

TP7.4: 20 residues within 4Å: Chain A: R.269, L.319, M.323, S.324, F.329, F.442, M.479, N.480, V.481 Chain B: F.361, Y.366, G.367, G.368, H.378, I.379, V.380 Chain D: R.224, K.255, H.256 Ligands: ACT.14 20 PLIP interactions: 6 interactions with chain B, 10 interactions with chain A, 4 interactions with chain D Hydrophobic interactions: B:F.361, B:Y.366, B:I.379, B:V.380, A:L.319, A:M.323 Hydrogen bonds: B:G.368, D:K.255 Salt bridges: B:H.378, A:R.269, D:R.224, D:K.255, D:K.255 Water bridges: A:R.269, A:R.269, A:R.269, A:R.269, A:R.269, A:R.269, A:R.269 TP7.9: 19 residues within 4Å: Chain A: R.224, K.255, H.256 Chain D: R.269, L.319, M.323, S.324, F.329, F.442, M.479, N.480, V.481 Chain E: F.361, Y.366, G.367, G.368, H.378, I.379 Ligands: ACT.6 16 PLIP interactions: 5 interactions with chain E, 6 interactions with chain D, 5 interactions with chain A Hydrophobic interactions: E:F.361, E:Y.366, E:I.379, D:M.323 Hydrogen bonds: E:G.368, A:K.255, A:K.255 Salt bridges: E:H.378, D:R.269, A:R.224, A:K.255, A:K.255 Water bridges: D:R.269, D:R.269, D:R.269, D:R.269

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

COM.5: 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: F43.8 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain A Water bridges: C:R.119, C:R.119 Salt bridges: C:R.119 Hydrogen bonds: A:Y.443 COM.15: 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: F43.1 3 PLIP interactions: 2 interactions with chain F, 1 interactions with chain D Water bridges: F:R.119 Salt bridges: F:R.119 Hydrogen bonds: D:Y.443

1 x NA: SODIUM ION(Non-functional Binders)

NA.7: 8 residues within 4Å: Chain A: R.101, S.214, R.215, C.217 Chain D: R.101, S.214, R.215, C.217 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:R.101, A:S.214, D:R.101

8 x XE: XENON(Non-covalent)(Covalent)

XE.10: 4 residues within 4Å: Chain A: Q.191, S.292, A.496, D.500 No protein-ligand interaction detected (PLIP) XE.11: 4 residues within 4Å: Chain B: M.177, A.202, L.213, F.424 No protein-ligand interaction detected (PLIP) XE.12: 4 residues within 4Å: Chain B: A.46, A.175, I.414, F.418 No protein-ligand interaction detected (PLIP) XE.13: 7 residues within 4Å: Chain B: L.330, T.354, F.358, T.381, A.388, I.389, V.392 No protein-ligand interaction detected (PLIP) XE.16: 4 residues within 4Å: Chain D: Q.191, S.292, A.496, D.500 No protein-ligand interaction detected (PLIP) XE.19: 5 residues within 4Å: Chain E: M.177, H.198, V.199, A.202, L.213 No protein-ligand interaction detected (PLIP) XE.20: 4 residues within 4Å: Chain E: A.46, A.175, I.414, F.418 No protein-ligand interaction detected (PLIP) XE.21: 6 residues within 4Å: Chain E: L.330, T.354, F.358, T.381, A.388, V.392 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

2022-04-06

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
D

B
B

E
E

C
C

F
F

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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