SMTL ID : 5g0r.1

METHYL-COENZYME M REDUCTASE I FROM METHANOTHERMOBACTER MARBURGENSIS EXPOSED TO 3-NITROOXYPROPANOL

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.25 Å

Oligo State

hetero-2-2-2-mer

Ligands

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

MG.1: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.2: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.5: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.6: 3 residues within 4Å: Chain A: K.11, F.14, E.15 6 PLIP interactions: 2 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:K.11, A:F.14, H2O.2, H2O.2, H2O.2, H2O.2 MG.8: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.9: 1 residues within 4Å: Chain A: D.177 No protein-ligand interaction detected (PLIP) MG.13: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.14: 1 residues within 4Å: Chain B: D.271 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.271, H2O.40, H2O.40, H2O.40 MG.16: 2 residues within 4Å: Chain C: E.30, K.135 5 PLIP interactions: 1 interactions with chain C, 4 Ligand-Water interactions Metal complexes: C:E.30, H2O.47, H2O.47, H2O.47, H2O.51 MG.17: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.18: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.21: 3 residues within 4Å: Chain D: K.11, F.14, E.15 6 PLIP interactions: 2 interactions with chain D, 4 Ligand-Water interactions Metal complexes: D:K.11, D:F.14, H2O.56, H2O.56, H2O.56, H2O.57 MG.23: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.24: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.25: 1 residues within 4Å: Chain E: D.147 5 PLIP interactions: 1 interactions with chain E, 4 Ligand-Water interactions Metal complexes: E:D.147, H2O.84, H2O.84, H2O.84, H2O.91 MG.26: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.28: 4 residues within 4Å: Chain E: D.99, D.100, T.101, N.102 5 PLIP interactions: 2 interactions with chain E, 3 Ligand-Water interactions Metal complexes: E:D.99, E:T.101, H2O.82, H2O.83, H2O.83 MG.29: 2 residues within 4Å: Chain F: E.30, K.135 5 PLIP interactions: 1 interactions with chain F, 4 Ligand-Water interactions Metal complexes: F:E.30, H2O.94, H2O.94, H2O.94, H2O.98

2 x F43: FACTOR 430(Non-covalent)

F43.3: 33 residues within 4Å: Chain A: A.144, V.145, V.146, Q.147, M.150, M.229, 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 38 PLIP interactions: 7 interactions with chain A, 15 interactions with chain F, 12 interactions with chain D, 3 interactions with chain E, 1 Ligand-Water interactions Hydrophobic interactions: A:Q.147, A:A.243, F:L.117, D:V.328, D:F.330, D:Y.333, D:Y.333, D:F.396, D:F.443 Hydrogen bonds: A:V.145, A:V.146, A:Q.147, A:Q.230, F:S.118, F:G.119, F:R.120, F:S.154, F:V.155, 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: A:A.243, F:S.118, F:S.118, F:G.152, F:H.156, F:G.157, F:G.157, F:H.158, D:T.331 Salt bridges: F:H.156, F:H.158 Metal complexes: H2O.70 F43.19: 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, M.229, Q.230, M.233, A.243 37 PLIP interactions: 16 interactions with chain C, 11 interactions with chain A, 7 interactions with chain D, 2 interactions with chain B, 1 Ligand-Water interactions, Hydrophobic interactions: C:L.117, A:V.328, A:F.330, A:Y.333, A:Y.333, A:F.396, A:F.443, D:Q.147, D:A.243 Hydrogen bonds: C:S.118, C:G.119, C:R.120, C:S.154, C:V.155, A:G.329, A:Q.332, A:Q.332, A:Y.333, D:V.145, D:V.146, D:Q.147, D:Q.230, B:I.366, B:Y.367 Water bridges: C:S.118, C:S.118, C:R.120, C:G.152, C:H.156, C:G.157, C:G.157, C:H.158, A:T.331, D:A.243 Salt bridges: C:H.156, C:H.158 Metal complexes: H2O.18

2 x TP7: Coenzyme B

TP7.4: 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 22 PLIP interactions: 7 interactions with chain D, 5 interactions with chain A, 10 interactions with chain B Hydrogen bonds: D:K.256, D:K.256, B:G.369 Water bridges: D:R.225, D:R.225, A:R.270, A:M.324, B:Y.367, B:G.369 Salt bridges: D:R.225, D:K.256, D:K.256, A:R.270, B:H.379 Hydrophobic interactions: A:M.324, A:F.330, B:F.362, B:F.362, B:Y.367, B:Y.367, B:I.380, B:V.381 TP7.20: 20 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.361, F.362, Y.367, G.368, G.369, H.379, I.380, V.381 20 PLIP interactions: 7 interactions with chain A, 8 interactions with chain E, 5 interactions with chain D Hydrogen bonds: A:K.256, A:K.256, E:G.369 Water bridges: A:R.225, A:R.225, D:R.270, D:R.270 Salt bridges: A:R.225, A:K.256, A:K.256, E:H.379, D:R.270 Hydrophobic interactions: E:F.362, E:F.362, E:Y.367, E:Y.367, E:I.380, E:V.381, D:M.324, D:F.330

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

NA.7: 4 residues within 4Å: Chain A: P.58, I.60, G.61, T.62 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:P.58 Water bridges: A:L.64 NA.10: 3 residues within 4Å: Chain A: H.131 Chain D: I.60, G.61 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:G.61, A:H.131 NA.22: 4 residues within 4Å: Chain D: P.58, I.60, G.61, T.62 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:T.62 Water bridges: D:L.64

1 x K: POTASSIUM ION(Non-covalent)

K.11: 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 D, 2 interactions with chain A Metal complexes: D:R.216, D:C.218, A:R.216, A:C.218

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

CL.12: 3 residues within 4Å: Chain A: I.60, G.61 Chain D: H.131 Ligand excluded by PLIP CL.15: 3 residues within 4Å: Chain B: R.235, A.300 Chain C: L.248 Ligand excluded by PLIP CL.27: 3 residues within 4Å: Chain E: R.235, A.300 Chain F: L.248 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Duin, E.C. et al., Mode of Action Uncovered for the Specific Reduction of Methane Emissions from Ruminants by the Small Molecule 3-Nitrooxypropanol. Proc.Natl.Acad.Sci.USA (2016)

Release Date

2016-04-13

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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