SMTL ID : 5n1q.1

METHYL-COENZYME M REDUCTASE III FROM METHANOTHERMOCOCCUS THERMOLITHOTROPHICUS AT 1.9 A RESOLUTION

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

hetero-2-2-2-mer

Ligands

2 x TP7: Coenzyme B

TP7.1: 19 residues within 4Å: Chain A: R.274, L.323, M.327, S.328, F.333, F.446, M.483, N.484, V.485 Chain B: F.362, Y.367, G.368, G.369, H.379, V.380, V.381 Chain D: R.229, K.260, H.261 20 PLIP interactions: 10 interactions with chain B, 5 interactions with chain D, 5 interactions with chain A Hydrophobic interactions: B:F.362, B:Y.367, B:V.380, B:V.381, A:M.327, A:F.333 Hydrogen bonds: B:G.369, D:K.260, D:K.260 Water bridges: B:Y.367, B:G.369, B:G.369, B:H.379, A:M.327 Salt bridges: B:H.379, D:R.229, D:K.260, D:K.260, A:R.274, A:R.274 TP7.8: 19 residues within 4Å: Chain A: R.229, K.260, H.261 Chain D: R.274, L.323, M.327, S.328, F.333, F.446, M.483, N.484, V.485 Chain E: F.362, Y.367, G.368, G.369, H.379, V.380, V.381 19 PLIP interactions: 5 interactions with chain D, 9 interactions with chain E, 5 interactions with chain A Hydrophobic interactions: D:M.327, D:F.333, E:F.362, E:Y.367, E:V.380, E:V.381 Water bridges: D:M.327, E:G.369, E:H.379, A:K.260 Salt bridges: D:R.274, D:R.274, E:H.379, A:R.229, A:K.260, A:K.260 Hydrogen bonds: E:Y.367, E:G.369, A:K.260

2 x F43: FACTOR 430(Non-covalent)

F43.2: 32 residues within 4Å: Chain A: A.148, V.149, V.150, Q.151, M.154, Q.234, M.237, A.247 Chain D: G.329, G.330, V.331, G.332, F.333, T.334, Q.335, Y.336, F.399, G.400, G.445, F.446 Chain E: S.365, I.366, Y.367 Chain F: L.120, S.121, G.122, A.157, T.158, V.159, H.160, H.162 Ligands: COM.4 37 PLIP interactions: 12 interactions with chain D, 8 interactions with chain A, 3 interactions with chain E, 14 interactions with chain F, Hydrophobic interactions: D:V.331, D:F.333, D:Y.336, D:Y.336, D:F.399, D:F.446, A:V.150, A:Q.151 Hydrogen bonds: D:V.331, D:G.332, D:Q.335, D:Q.335, D:Y.336, A:V.149, A:V.150, A:Q.151, A:Q.234, E:I.366, E:Y.367, E:Y.367, F:S.121, F:G.122, F:T.158, F:V.159 Water bridges: D:T.334, A:Q.151, A:A.247, F:S.121, F:S.121, F:H.160, F:H.160, F:H.160, F:G.161, F:G.161, F:H.162 Salt bridges: F:H.160, F:H.162 F43.7: 33 residues within 4Å: Chain A: G.329, G.330, V.331, G.332, F.333, T.334, Q.335, Y.336, F.399, G.400, G.445, F.446 Chain B: S.365, I.366, Y.367 Chain C: L.120, S.121, G.122, R.123, A.157, T.158, V.159, H.160, H.162 Chain D: A.148, V.149, V.150, Q.151, M.154, Q.234, M.237, A.247 Ligands: COM.6 36 PLIP interactions: 13 interactions with chain C, 3 interactions with chain B, 13 interactions with chain A, 7 interactions with chain D, Hydrogen bonds: C:S.121, C:G.122, C:T.158, C:V.159, B:I.366, B:Y.367, B:Y.367, A:V.331, A:G.332, A:Q.335, A:Q.335, A:Y.336, A:Y.336, D:V.149, D:V.150, D:Q.151, D:Q.234 Water bridges: C:S.121, C:S.121, C:H.160, C:H.160, C:G.161, C:G.161, C:H.162, A:T.334, D:Q.151 Salt bridges: C:H.160, C:H.162 Hydrophobic interactions: A:V.331, A:F.333, A:Y.336, A:Y.336, A:F.399, A:F.446, D:V.150, D:Q.151

1 x K: POTASSIUM ION(Non-covalent)

K.3: 8 residues within 4Å: Chain A: R.106, G.219, R.220, C.222 Chain D: R.106, G.219, R.220, C.222 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain A Metal complexes: D:G.219, D:R.220, D:C.222, A:R.220, A:C.222

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

COM.4: 9 residues within 4Å: Chain D: Y.336, F.446, Y.447 Chain E: F.361, S.365, Y.367 Chain F: L.120, R.123 Ligands: F43.2 3 PLIP interactions: 2 interactions with chain F, 1 interactions with chain D Hydrogen bonds: F:R.123, D:Y.447 Water bridges: F:R.123 COM.6: 9 residues within 4Å: Chain A: Y.336, F.446, Y.447 Chain B: F.361, S.365, Y.367 Chain C: L.120, R.123 Ligands: F43.7 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain A Water bridges: C:R.123, C:R.123 Salt bridges: C:R.123 Hydrogen bonds: A:Y.447

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 8 residues within 4Å: Chain B: L.121, E.122, A.124 Chain E: V.39, K.40, K.43, S.118, L.121 7 PLIP interactions: 2 interactions with chain B, 5 interactions with chain E Hydrogen bonds: B:L.121, E:V.39, E:K.43, E:S.118 Water bridges: B:K.43, E:K.40, E:E.122 GOL.9: 8 residues within 4Å: Chain A: K.39, L.73, M.74, G.87, D.88 Chain D: H.153, M.154, V.155 4 PLIP interactions: 1 interactions with chain D, 3 interactions with chain A Hydrogen bonds: D:H.153, A:M.74, A:G.87, A:D.88 GOL.11: 6 residues within 4Å: Chain A: V.126, Y.243, K.244 Chain F: H.45, R.86, R.197 5 PLIP interactions: 3 interactions with chain F, 2 interactions with chain A Hydrogen bonds: F:H.45, F:R.86, F:R.197, A:Y.243, A:K.244

1 x MG: MAGNESIUM ION(Non-covalent)

MG.10: 2 residues within 4Å: Chain E: T.292 Chain F: Q.6 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wagner, T. et al., Phylogenetic and Structural Comparisons of the Three Types of Methyl Coenzyme M Reductase from Methanococcales and Methanobacteriales. J.Bacteriol. (2017)

Release Date

2017-06-14

Peptides

METHYL-COENZYME M REDUCTASE III FROM METHANOTHERMOCOCCUS THERMOLITHOTROPHICUS SUBUNIT ALPHA: AD
METHYL-COENZYME M REDUCTASE III FROM METHANOTHERMOCOCCUS THERMOLITHOTROPHICUS SUBUNIT BETA: BE
METHYL-COENZYME M REDUCTASE III FROM METHANOTHERMOCOCCUS THERMOLITHOTROPHICUS 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 III FROM METHANOTHERMOCOCCUS THERMOLITHOTROPHICUS SUBUNIT ALPHA

METHYL-COENZYME M REDUCTASE III FROM METHANOTHERMOCOCCUS THERMOLITHOTROPHICUS SUBUNIT BETA

METHYL-COENZYME M REDUCTASE III FROM METHANOTHERMOCOCCUS THERMOLITHOTROPHICUS SUBUNIT GAMMA