SMTL ID : 5odi.1

Heterodisulfide reductase / [NiFe]-hydrogenase complex from Methanothermococcus thermolithotrophicus cocrystallized with CoM-SH

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

hetero-2-2-2-2-2-2-mer

Ligands

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

ACT.1: 6 residues within 4Å: Chain A: G.367, K.368, V.369, K.377, K.417, S.418 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:K.417 Hydrogen bonds: A:S.418 ACT.17: 3 residues within 4Å: Chain D: H.104, E.105, W.106 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:W.106 Salt bridges: D:H.104 ACT.25: 4 residues within 4Å: Chain G: G.141, V.142, T.143, N.229 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:T.143

2 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)

FAD.2: 36 residues within 4Å: Chain A: I.149, G.150, G.151, G.152, V.153, A.154, V.172, E.173, K.174, T.175, G.180, R.181, M.182, L.185, K.187, T.188, F.189, A.327, I.328, G.329, Y.330, A.352, L.353, E.356, Y.406, K.409, S.500, V.504, G.539, A.540, K.545, D.546, I.547, P.548, S.550 Chain G: K.524 29 PLIP interactions: 28 interactions with chain A, 1 interactions with chain G Hydrophobic interactions: A:L.185, A:Y.330, A:L.353, A:Y.406 Hydrogen bonds: A:G.151, A:G.151, A:G.152, A:A.154, A:K.174, A:R.181, A:R.181, A:M.182, A:F.189, A:F.189, A:Y.330, A:K.409, A:S.500, A:S.500, A:A.540, A:K.545, A:I.547, A:S.550, G:K.524 Water bridges: A:G.152, A:V.153, A:V.153, A:G.155, A:S.500 pi-Stacking: A:F.189 FAD.26: 33 residues within 4Å: Chain G: I.149, G.150, G.151, G.152, V.153, A.154, V.172, E.173, K.174, T.175, G.180, R.181, M.182, L.185, T.188, F.189, A.327, I.328, G.329, Y.330, L.353, E.356, Y.406, K.409, S.500, V.504, G.539, A.540, K.545, D.546, I.547, P.548, S.550 29 PLIP interactions: 29 interactions with chain G Hydrophobic interactions: G:L.185, G:Y.330, G:E.356, G:Y.406, G:Y.406 Hydrogen bonds: G:G.151, G:A.154, G:K.174, G:G.180, G:R.181, G:M.182, G:F.189, G:F.189, G:Y.330, G:K.409, G:S.500, G:S.500, G:A.540, G:K.545, G:I.547, G:S.550 Water bridges: G:G.152, G:G.152, G:T.175, G:R.181, G:Y.330, G:C.541, G:C.541 pi-Stacking: G:F.189

22 x SF4: IRON/SULFUR CLUSTER(Non-covalent)

SF4.3: 11 residues within 4Å: Chain A: Q.385, C.386, S.389, R.390, C.399, S.400, N.401, C.403, C.404, D.429, R.431 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.386, A:C.399, A:C.403, A:C.404 SF4.4: 10 residues within 4Å: Chain A: C.11, C.13, Y.44, M.45, C.46, A.70, C.71, H.76, R.100 Chain G: C.197 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain G, Metal complexes: A:C.11, A:C.13, A:C.46, A:C.71, G:C.197 SF4.5: 10 residues within 4Å: Chain A: C.594, A.598, C.617, K.618, G.619, C.620, G.621, T.622, C.623, P.624 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.594, A:C.617, A:C.620, A:C.623 SF4.6: 10 residues within 4Å: Chain A: C.584, G.586, C.587, G.588, V.589, C.590, A.610, C.627, S.629, L.632 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.584, A:C.587, A:C.590, A:C.627 SF4.7: 10 residues within 4Å: Chain A: C.256, P.257, I.258, A.273, C.293, I.294, E.295, C.296, G.297, C.299 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.256, A:C.293, A:C.296, A:C.299 SF4.8: 9 residues within 4Å: Chain A: C.246, T.247, G.248, C.249, G.250, Q.251, C.252, Y.286, C.303 5 PLIP interactions: 5 interactions with chain A, pi-Cation interactions: A:Y.286 Metal complexes: A:C.246, A:C.249, A:C.252, A:C.303 SF4.14: 9 residues within 4Å: Chain C: C.34, Y.35, Q.36, C.37, G.38, C.40, R.55, C.87, V.91 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:C.34, C:C.37, C:C.40, C:C.87 SF4.15: 11 residues within 4Å: Chain C: C.44, P.45, Y.52, T.54, C.77, T.78, T.79, C.80, Y.81, C.83, T.94 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:C.44, C:C.77, C:C.80, C:C.83 SF4.19: 11 residues within 4Å: Chain E: G.11, C.12, G.14, C.15, E.57, T.84, C.85, G.148, C.149, P.150 Chain F: H.163 6 PLIP interactions: 5 interactions with chain E, 1 Ligand-Water interactions, Salt bridges: E:E.57 Metal complexes: E:C.12, E:C.15, E:C.85, E:C.149, H2O.9 SF4.20: 10 residues within 4Å: Chain E: L.176, C.224, P.227, C.228, C.235, S.236, G.237, C.238, S.239 Chain F: R.160 4 PLIP interactions: 4 interactions with chain E, Metal complexes: E:C.224, E:C.228, E:C.235, E:C.238 SF4.21: 10 residues within 4Å: Chain E: C.177, C.180, R.182, K.184, C.207, L.208, C.215, G.217, I.218, P.229 4 PLIP interactions: 4 interactions with chain E, Metal complexes: E:C.177, E:C.180, E:C.207, E:C.215 SF4.27: 11 residues within 4Å: Chain A: C.197 Chain G: C.11, C.13, I.17, Y.44, M.45, C.46, A.70, C.71, H.76, R.100 4 PLIP interactions: 4 interactions with chain G, Metal complexes: G:C.11, G:C.13, G:C.46, G:C.71 SF4.28: 11 residues within 4Å: Chain G: Q.385, C.386, S.389, R.390, C.399, S.400, N.401, C.403, C.404, D.429, R.431 4 PLIP interactions: 4 interactions with chain G, Metal complexes: G:C.386, G:C.399, G:C.403, G:C.404 SF4.29: 8 residues within 4Å: Chain G: C.246, T.247, G.248, C.249, G.250, C.252, Y.286, C.303 4 PLIP interactions: 4 interactions with chain G, Metal complexes: G:C.246, G:C.249, G:C.252, G:C.303 SF4.30: 7 residues within 4Å: Chain G: C.256, P.257, A.273, C.293, C.296, G.297, C.299 4 PLIP interactions: 4 interactions with chain G, Metal complexes: G:C.256, G:C.293, G:C.296, G:C.299 SF4.31: 9 residues within 4Å: Chain G: C.594, A.598, P.599, C.617, K.618, G.619, C.620, G.621, C.623 4 PLIP interactions: 4 interactions with chain G, Metal complexes: G:C.594, G:C.617, G:C.620, G:C.623 SF4.32: 12 residues within 4Å: Chain G: V.579, C.584, G.585, G.586, C.587, G.588, C.590, A.610, C.627, S.629, L.632 Chain K: N.175 4 PLIP interactions: 4 interactions with chain G, Metal complexes: G:C.584, G:C.587, G:C.590, G:C.627 SF4.38: 10 residues within 4Å: Chain I: C.34, Y.35, Q.36, C.37, G.38, T.39, C.40, R.55, C.87, V.91 4 PLIP interactions: 4 interactions with chain I, Metal complexes: I:C.34, I:C.37, I:C.40, I:C.87 SF4.39: 12 residues within 4Å: Chain I: C.44, P.45, Y.52, T.54, C.77, T.78, T.79, C.80, Y.81, C.83, T.94, I.97 4 PLIP interactions: 4 interactions with chain I, Metal complexes: I:C.44, I:C.77, I:C.80, I:C.83 SF4.41: 10 residues within 4Å: Chain K: C.12, G.14, C.15, E.57, T.84, C.85, C.149, P.150 Chain L: R.59, H.163 5 PLIP interactions: 5 interactions with chain K, Salt bridges: K:E.57 Metal complexes: K:C.12, K:C.15, K:C.85, K:C.149 SF4.42: 10 residues within 4Å: Chain K: L.176, C.224, P.227, C.228, C.235, S.236, G.237, C.238, S.239 Chain L: R.160 4 PLIP interactions: 4 interactions with chain K, Metal complexes: K:C.224, K:C.228, K:C.235, K:C.238 SF4.43: 10 residues within 4Å: Chain K: C.177, C.180, K.184, C.207, L.208, L.209, C.215, G.217, I.218, P.229 4 PLIP interactions: 4 interactions with chain K, Metal complexes: K:C.177, K:C.180, K:C.207, K:C.215

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 7 residues within 4Å: Chain A: V.337, R.338, E.340, K.393 Chain H: E.168 Chain I: E.85, R.86 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain H Hydrogen bonds: A:V.337, A:K.393, H:E.168 Water bridges: H:E.168 GOL.10: 7 residues within 4Å: Chain A: Y.427, Y.441, F.452, L.477 Chain C: C.34, Y.35, Q.36 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:Y.427, A:Y.427, A:Y.441, A:Y.441, A:F.452 Water bridges: C:R.89 GOL.33: 8 residues within 4Å: Chain G: Y.427, Y.441, F.452, L.477 Chain I: C.34, Y.35, Q.36, L.62 4 PLIP interactions: 3 interactions with chain G, 1 interactions with chain I Hydrogen bonds: G:Y.427, I:C.34 Water bridges: G:F.452, G:F.452 GOL.37: 5 residues within 4Å: Chain H: R.14, Y.15, L.236, V.279, Q.281 1 PLIP interactions: 1 interactions with chain H Hydrogen bonds: H:R.14 GOL.44: 3 residues within 4Å: Chain K: A.87, S.137, F.145 1 PLIP interactions: 1 interactions with chain K Hydrogen bonds: K:S.137

4 x 9S8: Non-cubane [4Fe-4S]-cluster(Non-covalent)

9S8.11: 10 residues within 4Å: Chain B: G.8, C.9, C.41, C.42, A.44, C.78, G.80, C.81, F.233 Chain C: A.127 6 PLIP interactions: 6 interactions with chain B Metal complexes: B:C.9, B:C.41, B:C.42, B:C.78, B:C.81, B:C.81 9S8.12: 13 residues within 4Å: Chain B: N.79, H.150, G.152, C.153, H.154, C.193, C.194, G.197, C.231, F.233, C.234 Chain C: T.78 Ligands: COM.13 5 PLIP interactions: 5 interactions with chain B, Metal complexes: B:C.153, B:C.193, B:C.194, B:C.231, B:C.234 9S8.34: 8 residues within 4Å: Chain H: G.8, C.9, C.41, C.42, C.78, C.81, F.233 Chain I: A.127 6 PLIP interactions: 6 interactions with chain H, Metal complexes: H:C.9, H:C.41, H:C.42, H:C.78, H:C.81, H:C.81 9S8.35: 11 residues within 4Å: Chain H: H.150, C.153, H.154, C.193, C.194, G.197, C.231, F.233, C.234 Chain I: T.78 Ligands: COM.36 5 PLIP interactions: 5 interactions with chain H, Metal complexes: H:C.153, H:C.193, H:C.194, H:C.231, H:C.234

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

COM.13: 9 residues within 4Å: Chain B: A.44, P.45, G.46, G.80, H.154, G.198, G.199, F.233 Ligands: 9S8.12 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.46, B:G.198, B:G.199 Water bridges: B:V.47 COM.36: 10 residues within 4Å: Chain H: A.44, P.45, G.46, G.80, H.154, G.198, G.199, C.231, F.233 Ligands: 9S8.35 4 PLIP interactions: 4 interactions with chain H Hydrogen bonds: H:G.46, H:G.198, H:G.199 Salt bridges: H:H.154

2 x FES: FE2/S2 (INORGANIC) CLUSTER(Non-covalent)

FES.16: 9 residues within 4Å: Chain D: C.13, M.41, C.42, S.43, C.67, C.72, H.73, Y.74, N.78 4 PLIP interactions: 4 interactions with chain D, Metal complexes: D:C.13, D:C.42, D:C.67, D:C.72 FES.40: 9 residues within 4Å: Chain J: C.13, M.41, C.42, S.43, C.67, C.72, H.73, Y.74, N.78 4 PLIP interactions: 4 interactions with chain J, Metal complexes: J:C.13, J:C.42, J:C.67, J:C.72

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.18: 8 residues within 4Å: Chain D: W.4, K.7, G.58, D.60, P.131, C.132, K.135, E.136 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:W.4, D:G.58

2 x NFU: formyl[bis(hydrocyanato-1kappaC)]ironnickel(Fe-Ni)(Non-covalent)

NFU.22: 12 residues within 4Å: Chain F: C.61, C.64, H.68, A.373, P.374, R.375, L.378, V.397, A.398, T.399, C.442, C.445 11 PLIP interactions: 11 interactions with chain F Hydrogen bonds: F:R.375, F:R.375, F:T.399, F:T.399, F:C.442 Metal complexes: F:C.61, F:C.64, F:C.64, F:C.442, F:C.445, F:C.445 NFU.45: 12 residues within 4Å: Chain L: C.61, C.64, H.68, A.373, P.374, R.375, L.378, V.397, A.398, T.399, C.442, C.445 10 PLIP interactions: 10 interactions with chain L Hydrogen bonds: L:R.375, L:R.375, L:A.398, L:T.399 Metal complexes: L:C.61, L:C.64, L:C.64, L:C.442, L:C.445, L:C.445

2 x FE: FE (III) ION(Non-covalent)

FE.23: 4 residues within 4Å: Chain F: E.42, K.273, L.395, H.448 5 PLIP interactions: 3 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:E.42, F:L.395, F:H.448, H2O.10, H2O.10 FE.46: 4 residues within 4Å: Chain L: E.42, K.273, L.395, H.448 5 PLIP interactions: 3 interactions with chain L, 2 Ligand-Water interactions Metal complexes: L:E.42, L:L.395, L:H.448, H2O.20, H2O.20

1 x PE3: 3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL(Non-functional Binders)

PE3.24: 7 residues within 4Å: Chain A: Q.144, M.165, G.166, F.167, A.566 Chain G: M.165, F.167 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wagner, T. et al., Methanogenic heterodisulfide reductase (HdrABC-MvhAGD) uses two noncubane [4Fe-4S] clusters for reduction. Science (2017)

Release Date

2017-08-30

Peptides

Heterodisulfide reductase, subunit A: AG
Heterodisulfide reductase, subunit B: BH
Heterodisulfide reductase, subunit C: CI
Methyl-viologen reducing hydrogenase, subunit D: DJ
Methyl-viologen reducing hydrogenase, subunit G: EK
Methyl-viologen reducing hydrogenase, subunit A: FL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

G
G

B
B

H
H

C
C

I
I

D
D

J
J

E
E

K
K

F
F

L
L

Heterodisulfide reductase, subunit A

Heterodisulfide reductase, subunit B

Heterodisulfide reductase, subunit C

Methyl-viologen reducing hydrogenase, subunit D

Methyl-viologen reducing hydrogenase, subunit G

Methyl-viologen reducing hydrogenase, subunit A

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