SMTL ID : 7b2h.1

Crystal structure of the methyl-coenzyme M reductase from Methanothermobacter Marburgensis derivatized with xenon

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.12 Å

Oligo State

hetero-2-2-2-mer

Ligands

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

COM.1: 9 residues within 4Å: Chain A: Y.333, F.443, Y.444 Chain B: F.361, S.365, Y.367 Chain C: L.117, R.120 Ligands: F43.8 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain C Hydrogen bonds: A:Y.444 Water bridges: C:R.120, C:R.120 Salt bridges: C:R.120 COM.30: 9 residues within 4Å: Chain D: Y.333, F.443, Y.444 Chain E: F.361, S.365, Y.367 Chain F: L.117, R.120 Ligands: F43.29 4 PLIP interactions: 3 interactions with chain F, 1 interactions with chain D Water bridges: F:R.120, F:R.120 Salt bridges: F:R.120 Hydrogen bonds: D:Y.444

2 x TP7: Coenzyme B

TP7.2: 20 residues within 4Å: Chain A: R.270, L.320, M.324, S.325, F.330, F.443, M.480, N.481, V.482 Chain B: F.361, F.362, Y.367, G.368, G.369, H.379, I.380, V.381 Chain D: R.225, K.256, H.257 21 PLIP interactions: 5 interactions with chain A, 10 interactions with chain B, 6 interactions with chain D Hydrophobic interactions: A:M.324, A:F.330, B:F.362, B:F.362, B:Y.367, B:I.380, B:V.381 Water bridges: A:R.270, A:M.324, B:Y.367, B:G.369, D:R.225, D:R.225 Salt bridges: A:R.270, B:H.379, D:R.225, D:K.256, D:K.256 Hydrogen bonds: B:Y.367, B:G.369, D:K.256 TP7.31: 19 residues within 4Å: Chain A: R.225, K.256, H.257 Chain D: R.270, L.320, M.324, S.325, F.330, F.443, M.480, N.481, V.482 Chain E: F.362, Y.367, G.368, G.369, H.379, I.380, V.381 18 PLIP interactions: 2 interactions with chain D, 10 interactions with chain E, 6 interactions with chain A Hydrophobic interactions: D:M.324, E:F.362, E:F.362, E:Y.367, E:I.380, E:V.381 Salt bridges: D:R.270, E:H.379, A:R.225, A:K.256, A:K.256 Hydrogen bonds: E:Y.367, E:G.369, A:K.256 Water bridges: E:G.369, E:H.379, A:R.225, A:R.225

4 x K: POTASSIUM ION(Non-covalent)

K.3: 8 residues within 4Å: Chain A: R.102, S.215, R.216, C.218 Chain D: R.102, S.215, R.216, C.218 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain D Metal complexes: A:R.216, A:C.218, D:R.216, D:C.218 K.15: 3 residues within 4Å: Chain A: P.58, I.60, T.62 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:P.58, A:I.60, A:T.62, H2O.6 K.28: 5 residues within 4Å: Chain B: W.302, N.303, P.345, S.346, F.349 No protein-ligand interaction detected (PLIP) K.38: 4 residues within 4Å: Chain A: A.144, V.145 Chain D: I.60, T.62 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain A Metal complexes: D:T.62, A:A.144

9 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.4: 2 residues within 4Å: Chain A: G.52, P.54 1 PLIP interactions: 1 interactions with chain A Water bridges: A:A.49 PEG.5: 3 residues within 4Å: Chain A: D.160, V.519, P.539 No protein-ligand interaction detected (PLIP) PEG.17: 4 residues within 4Å: Chain B: K.61, A.66 Chain D: E.199, P.507 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:K.61, B:A.66, D:E.199 PEG.18: 3 residues within 4Å: Chain B: M.150, Y.151 Chain F: Q.243 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:Q.243 PEG.33: 2 residues within 4Å: Chain D: N.42, K.45 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.42, D:K.45 PEG.34: 2 residues within 4Å: Chain D: E.46, K.50 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:E.46 PEG.35: 4 residues within 4Å: Chain D: T.79, N.524, G.527, L.534 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.524 PEG.40: 5 residues within 4Å: Chain E: G.402, Q.404, M.405 Chain F: V.52 Ligands: XE.44 No protein-ligand interaction detected (PLIP) PEG.50: 2 residues within 4Å: Chain F: E.232, R.236 No protein-ligand interaction detected (PLIP)

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 2 residues within 4Å: Chain A: A.544, T.547 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.547

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

EDO.7: 2 residues within 4Å: Chain A: P.71, Y.80 No protein-ligand interaction detected (PLIP)

2 x F43: FACTOR 430(Non-covalent)

F43.8: 33 residues within 4Å: Chain A: G.326, G.327, V.328, G.329, F.330, T.331, Q.332, Y.333, F.396, G.397, G.442, F.443 Chain B: S.365, I.366, Y.367 Chain C: L.117, S.118, G.119, R.120, K.153, S.154, V.155, H.156, H.158 Chain D: A.144, V.145, V.146, Q.147, M.150, Q.230, M.233, A.243 Ligands: COM.1 31 PLIP interactions: 10 interactions with chain A, 2 interactions with chain B, 5 interactions with chain D, 14 interactions with chain C, Hydrophobic interactions: A:V.328, A:F.330, A:Y.333, A:Y.333, A:F.443 Hydrogen bonds: A:G.329, A:Q.332, A:Q.332, A:Y.333, B:I.366, B:Y.367, D:V.145, D:V.146, D:Q.147, D:Q.230, C:S.118, C:G.119, C:R.120, C:S.154, C:V.155 Water bridges: A:T.331, D:Q.147, C:S.118, C:S.118, C:H.156, C:H.156, C:G.157, C:G.157, C:G.157 Salt bridges: C:H.156, C:H.158 F43.29: 33 residues within 4Å: Chain A: A.144, V.145, V.146, Q.147, M.150, Q.230, M.233, A.243 Chain D: G.326, G.327, V.328, G.329, F.330, T.331, Q.332, Y.333, F.396, G.397, G.442, F.443 Chain E: S.365, I.366, Y.367 Chain F: L.117, S.118, G.119, R.120, K.153, S.154, V.155, H.156, H.158 Ligands: COM.30 33 PLIP interactions: 14 interactions with chain F, 5 interactions with chain A, 11 interactions with chain D, 3 interactions with chain E, Hydrophobic interactions: F:V.155, D:V.328, D:F.330, D:Y.333, D:Y.333, D:F.443 Hydrogen bonds: F:S.118, F:G.119, F:R.120, F:S.154, F:V.155, A:V.145, A:V.146, A:Q.147, A:Q.230, D:G.329, D:Q.332, D:Q.332, D:Y.333, D:Y.333, E:I.366, E:Y.367, E:Y.367 Water bridges: F:S.118, F:S.118, F:H.156, F:H.158, F:H.158, F:H.158, A:A.143, D:T.331 Salt bridges: F:H.156, F:H.158

15 x MG: MAGNESIUM ION(Non-covalent)

MG.9: 1 residues within 4Å: Chain A: E.20 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.20, H2O.8, H2O.8 MG.10: 1 residues within 4Å: Chain A: E.19 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.19 MG.11: 3 residues within 4Å: Chain A: V.269, R.270 Chain D: E.275 4 PLIP interactions: 1 interactions with chain A, 1 interactions with chain D, 2 Ligand-Water interactions Metal complexes: A:V.269, D:E.275, H2O.17, H2O.23 MG.12: 1 residues within 4Å: Chain A: D.356 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.356 MG.16: 1 residues within 4Å: Chain B: D.271 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.271, H2O.11, H2O.12 MG.19: 2 residues within 4Å: Chain B: D.147, V.148 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.147, H2O.29 MG.20: 2 residues within 4Å: Chain B: D.13, E.427 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.13 MG.21: 1 residues within 4Å: Chain B: K.3 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:K.3, H2O.11 MG.32: 4 residues within 4Å: Chain D: K.11, F.14, E.15, E.16 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:K.11, D:F.14 MG.36: 1 residues within 4Å: Chain D: E.383 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:E.383 MG.39: 3 residues within 4Å: Chain C: E.249 Chain E: D.147, V.148 4 PLIP interactions: 1 interactions with chain C, 1 interactions with chain E, 2 Ligand-Water interactions Metal complexes: C:E.249, E:D.147, H2O.25, H2O.26 MG.41: 2 residues within 4Å: Chain E: E.19, E.20 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:E.19 MG.42: 1 residues within 4Å: Chain E: D.13 3 PLIP interactions: 2 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:D.13, E:D.13, H2O.25 MG.43: 1 residues within 4Å: Chain E: D.271 2 PLIP interactions: 1 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:D.271, H2O.27 MG.49: 2 residues within 4Å: Chain F: E.30, K.135 2 PLIP interactions: 1 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:E.30, H2O.30

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

XE.13: 5 residues within 4Å: Chain A: Q.192, S.293, Y.297, A.497, D.501 No protein-ligand interaction detected (PLIP) XE.22: 2 residues within 4Å: Chain B: F.349 Chain C: N.247 No protein-ligand interaction detected (PLIP) XE.23: 2 residues within 4Å: Chain B: Q.40, F.121 No protein-ligand interaction detected (PLIP) XE.24: 5 residues within 4Å: Chain B: G.402, T.403, Q.404, M.405 Chain C: V.52 No protein-ligand interaction detected (PLIP) XE.25: 4 residues within 4Å: Chain B: A.47, A.176, I.415, F.419 No protein-ligand interaction detected (PLIP) XE.26: 5 residues within 4Å: Chain B: A.135, T.136, K.157 Chain D: I.460, G.462 No protein-ligand interaction detected (PLIP) XE.37: 4 residues within 4Å: Chain D: Q.192, S.293, Y.297, D.501 No protein-ligand interaction detected (PLIP) XE.44: 5 residues within 4Å: Chain E: G.402, T.403, Q.404, M.405 Ligands: PEG.40 No protein-ligand interaction detected (PLIP) XE.45: 4 residues within 4Å: Chain E: M.178, H.199, A.203, L.214 No protein-ligand interaction detected (PLIP) XE.46: 4 residues within 4Å: Chain E: A.47, A.176, I.415, F.419 No protein-ligand interaction detected (PLIP) XE.47: 5 residues within 4Å: Chain A: I.460, G.462 Chain E: A.135, T.136, K.157 No protein-ligand interaction detected (PLIP) XE.51: 2 residues within 4Å: Chain E: F.349 Chain F: N.247 No protein-ligand interaction detected (PLIP)

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.14: 7 residues within 4Å: Chain A: K.164, A.179, D.516, N.517 Chain D: R.51, G.52, I.53 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:N.517, D:R.51 Water bridges: A:K.164, A:K.164 Salt bridges: A:K.164

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.27: 5 residues within 4Å: Chain B: D.12, D.13, Q.210, L.429, K.430 Ligand excluded by PLIP CL.48: 2 residues within 4Å: Chain E: R.235, A.300 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hahn, C.J. et al., Crystal structure of a key enzyme for anaerobic ethane activation. Science (2021)

Release Date

2021-07-14

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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