- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.20 Å
- Oligo State
- hetero-2-2-2-2-2-2-mer
- Ligands
- 2 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)
- 22 x SF4: IRON/SULFUR CLUSTER(Non-covalent)
SF4.2: 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
SF4.3: 10 residues within 4Å:- Chain A: C.246, T.247, G.248, C.249, G.250, Q.251, C.252, Y.286, C.303, P.305
4 PLIP interactions:4 interactions with chain A,- pi-Cation interactions: A:Y.286
- Metal complexes: A:C.249, A:C.252, A:C.303
SF4.4: 10 residues within 4Å:- Chain A: C.256, A.273, I.274, C.293, I.294, E.295, C.296, G.297, C.299, F.310
4 PLIP interactions:4 interactions with chain A,- Metal complexes: A:C.256, A:C.293, A:C.296, A:C.299
SF4.5: 12 residues within 4Å:- Chain A: C.11, C.13, I.17, Y.44, M.45, C.46, A.70, C.71, H.76, F.80, 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
SF4.6: 12 residues within 4Å:- Chain A: A.577, C.594, Y.596, A.598, P.599, C.617, K.618, G.619, C.620, G.621, T.622, C.623
4 PLIP interactions:4 interactions with chain A,- Metal complexes: A:C.594, A:C.617, A:C.620, A:C.623
SF4.7: 13 residues within 4Å:- Chain A: V.579, C.584, G.586, C.587, G.588, V.589, C.590, A.610, C.627, P.628, S.629, L.632
- Chain E: N.175
4 PLIP interactions:4 interactions with chain A,- Metal complexes: A:C.584, A:C.587, A:C.590, A:C.627
SF4.14: 13 residues within 4Å:- Chain C: C.34, Y.35, Q.36, C.37, G.38, T.39, C.40, R.55, C.87, P.88, R.89, V.91, V.93
4 PLIP interactions:4 interactions with chain C,- Metal complexes: C:C.34, C:C.37, C:C.40, C:C.87
SF4.15: 12 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, I.97
4 PLIP interactions:4 interactions with chain C,- Metal complexes: C:C.44, C:C.77, C:C.80, C:C.83
SF4.20: 12 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: R.59, H.163
5 PLIP interactions:5 interactions with chain E,- Salt bridges: E:E.57
- Metal complexes: E:C.12, E:C.15, E:C.85, E:C.149
SF4.21: 13 residues within 4Å:- Chain E: L.176, T.220, C.224, A.226, P.227, C.228, P.229, 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
SF4.22: 11 residues within 4Å:- Chain E: L.176, C.177, C.180, R.182, K.184, C.207, L.208, L.209, C.215, G.217, I.218
4 PLIP interactions:4 interactions with chain E,- Metal complexes: E:C.177, E:C.180, E:C.207, E:C.215
SF4.32: 12 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
- Ligands: FE.30
4 PLIP interactions:4 interactions with chain G,- Metal complexes: G:C.11, G:C.13, G:C.46, G:C.71
SF4.33: 12 residues within 4Å:- Chain G: Q.385, C.386, S.389, R.390, C.399, S.400, N.401, V.402, 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
SF4.34: 11 residues within 4Å:- Chain G: I.241, C.246, T.247, G.248, C.249, G.250, Q.251, C.252, Y.286, C.303, I.308
5 PLIP interactions:5 interactions with chain G,- pi-Cation interactions: G:Y.286
- Metal complexes: G:C.246, G:C.249, G:C.252, G:C.303
SF4.35: 14 residues within 4Å:- Chain G: C.256, P.257, I.258, A.273, I.274, I.288, C.293, I.294, E.295, C.296, G.297, L.298, C.299, F.310
4 PLIP interactions:4 interactions with chain G,- Metal complexes: G:C.256, G:C.293, G:C.296, G:C.299
SF4.36: 13 residues within 4Å:- Chain G: A.577, C.594, Y.596, A.598, P.599, C.617, K.618, G.619, C.620, G.621, T.622, C.623, P.624
4 PLIP interactions:4 interactions with chain G,- Metal complexes: G:C.594, G:C.617, G:C.620, G:C.623
SF4.37: 13 residues within 4Å:- Chain G: V.579, C.584, G.586, C.587, G.588, V.589, C.590, A.610, C.627, P.628, 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
SF4.42: 12 residues within 4Å:- Chain I: C.34, Y.35, Q.36, C.37, G.38, T.39, C.40, R.55, C.87, R.89, V.91, V.93
4 PLIP interactions:4 interactions with chain I,- Metal complexes: I:C.34, I:C.37, I:C.40, I:C.87
SF4.43: 11 residues within 4Å:- Chain I: C.44, 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
SF4.47: 12 residues within 4Å:- Chain K: G.11, C.12, G.14, C.15, E.57, T.84, C.85, G.148, 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
SF4.48: 12 residues within 4Å:- Chain K: L.176, T.220, C.224, P.227, C.228, P.229, 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
SF4.49: 10 residues within 4Å:- Chain K: C.177, C.180, R.182, K.184, C.207, L.208, L.209, C.215, G.217, I.218
4 PLIP interactions:4 interactions with chain K,- Metal complexes: K:C.177, K:C.180, K:C.207, K:C.215
- 6 x GOL: GLYCEROL(Non-functional Binders)
GOL.8: 7 residues within 4Å:- Chain A: V.337, R.338, E.339, E.340
- Chain H: E.168
- Chain I: E.85, R.86
5 PLIP interactions:3 interactions with chain A, 1 interactions with chain I, 1 interactions with chain H- Hydrogen bonds: A:V.337, A:E.339, I:E.85, H:E.168
- Water bridges: A:E.339
GOL.9: 8 residues within 4Å:- Chain A: Y.427, Y.441, A.445, F.452, L.477
- Chain C: C.34, Y.35, Q.36
5 PLIP interactions:3 interactions with chain A, 2 interactions with chain C- Hydrogen bonds: A:Y.427, A:Y.427, C:C.34
- Water bridges: A:F.452, C:R.89
GOL.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:D.60, D:E.136
GOL.44: 7 residues within 4Å:- Chain G: Y.427, Y.441, F.452, L.477
- Chain I: C.34, Y.35, Q.36
3 PLIP interactions:2 interactions with chain G, 1 interactions with chain I- Hydrogen bonds: G:Y.427
- Water bridges: G:F.452, I:R.59
GOL.45: 4 residues within 4Å:- Chain G: Q.447, Y.448, G.449
- Chain I: K.32
1 PLIP interactions:1 interactions with chain I- Hydrogen bonds: I:K.32
GOL.50: 3 residues within 4Å:- Chain K: A.87, V.142, F.145
2 PLIP interactions:2 interactions with chain K- Water bridges: K:A.87, K:S.137
- 4 x 9S8: Non-cubane [4Fe-4S]-cluster(Non-covalent)
9S8.10: 9 residues within 4Å:- Chain B: G.8, C.9, I.10, C.41, C.42, C.78, 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
9S8.11: 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.12
7 PLIP interactions:6 interactions with chain B, 1 Ligand-Water interactions,- Metal complexes: B:C.153, B:C.193, B:C.194, B:C.231, B:C.234, B:C.234, H2O.8
9S8.38: 9 residues within 4Å:- Chain H: G.8, C.9, I.10, C.41, C.42, C.78, G.80, C.81
- Ligands: TP7.41
5 PLIP interactions:5 interactions with chain H,- Metal complexes: H:C.9, H:C.41, H:C.42, H:C.78, H:C.81
9S8.39: 12 residues within 4Å:- Chain H: N.79, G.152, C.153, H.154, C.193, C.194, G.197, C.231, F.233, C.234
- Chain I: T.78
- Ligands: COM.40
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.12: 10 residues within 4Å:- Chain B: A.44, P.45, G.46, G.80, H.154, G.198, G.199, C.231, F.233
- Ligands: 9S8.11
5 PLIP interactions:5 interactions with chain B- Hydrogen bonds: B:G.46, B:G.198, B:G.199
- Water bridges: B:V.47, B:V.47
COM.40: 13 residues within 4Å:- Chain H: A.44, P.45, G.46, V.47, G.80, H.154, G.197, G.198, C.231, F.233
- Chain I: T.79
- Ligands: 9S8.39, TP7.41
5 PLIP interactions:5 interactions with chain H- Hydrogen bonds: H:G.46, H:V.47, H:G.198
- Water bridges: H:G.199
- Salt bridges: H:H.154
- 1 x SO4: SULFATE ION(Non-functional Binders)
- 2 x FES: FE2/S2 (INORGANIC) CLUSTER(Non-covalent)
FES.16: 10 residues within 4Å:- Chain D: C.13, W.15, 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.46: 11 residues within 4Å:- Chain J: C.13, W.15, M.41, C.42, S.43, G.66, 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
- 4 x ACT: ACETATE ION(Non-functional Binders)
ACT.17: 3 residues within 4Å:- Chain D: H.104, E.105, W.106
1 PLIP interactions:1 interactions with chain D- Salt bridges: D:H.104
ACT.19: 3 residues within 4Å:- Chain E: A.87, S.137, F.145
1 PLIP interactions:1 interactions with chain E- Hydrogen bonds: E:S.137
ACT.26: 6 residues within 4Å:- Chain E: T.111, I.112
- Chain F: H.381, K.383, T.393, N.394
7 PLIP interactions:2 interactions with chain E, 5 interactions with chain F- Hydrogen bonds: E:I.112, F:T.393
- Salt bridges: E:K.106, F:H.381, F:K.383
- Hydrophobic interactions: F:N.394
- Water bridges: F:T.393
ACT.29: 5 residues within 4Å:- Chain G: G.141, V.142, T.143, G.228, N.229
1 PLIP interactions:1 interactions with chain G- Hydrogen bonds: G:T.143
- 2 x NFU: formyl[bis(hydrocyanato-1kappaC)]ironnickel(Fe-Ni)(Non-covalent)
NFU.23: 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
10 PLIP interactions:10 interactions with chain F- Hydrogen bonds: F:R.375, F:R.375, F:T.399, F:T.399
- Metal complexes: F:C.61, F:C.64, F:C.64, F:C.442, F:C.445, F:C.445
NFU.51: 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
9 PLIP interactions:9 interactions with chain L- Hydrogen bonds: L:R.375, L:R.375, L:T.399
- Metal complexes: L:C.61, L:C.64, L:C.64, L:C.442, L:C.445, L:C.445
- 4 x PE3: 3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL(Non-functional Binders)
PE3.24: 6 residues within 4Å:- Chain F: L.206, E.207, K.210, E.312, F.317, Y.329
3 PLIP interactions:3 interactions with chain F- Hydrophobic interactions: F:E.312
- Hydrogen bonds: F:K.210, F:K.210
PE3.25: 5 residues within 4Å:- Chain F: M.117, H.136, E.138, I.139, L.205
1 PLIP interactions:1 interactions with chain F- Hydrogen bonds: F:E.138
PE3.28: 8 residues within 4Å:- Chain A: Q.144, M.165, G.166, F.167, A.566
- Chain G: M.165, G.166, F.167
No protein-ligand interaction detected (PLIP)PE3.52: 6 residues within 4Å:- Chain L: L.206, E.207, K.210, E.316, F.317, Y.329
1 PLIP interactions:1 interactions with chain L- Hydrophobic interactions: L:E.316
- 3 x FE: FE (III) ION(Non-covalent)
FE.27: 4 residues within 4Å:- Chain F: E.42, K.273, L.395, H.448
6 PLIP interactions:3 interactions with chain F, 3 Ligand-Water interactions- Metal complexes: F:E.42, F:L.395, F:H.448, H2O.17, H2O.18, H2O.18
FE.30: 4 residues within 4Å:- Chain A: C.197
- Chain G: C.46, H.76
- Ligands: SF4.32
3 PLIP interactions:3 interactions with chain G- Metal complexes: G:C.46, G:H.76, G:H.76
FE.53: 4 residues within 4Å:- Chain L: E.42, K.273, L.395, H.448
6 PLIP interactions:3 interactions with chain L, 3 Ligand-Water interactions- Metal complexes: L:E.42, L:L.395, L:H.448, H2O.37, H2O.38, H2O.38
- 1 x TP7: Coenzyme B
TP7.41: 12 residues within 4Å:- Chain H: I.10, R.14, A.44, R.201, A.202, F.233, L.236, R.240
- Chain I: T.117, V.128
- Ligands: 9S8.38, COM.40
11 PLIP interactions:2 interactions with chain I, 9 interactions with chain H- Hydrophobic interactions: I:T.117, I:V.128, H:I.10, H:A.44, H:F.233, H:F.233, H:F.233, H:L.236
- Salt bridges: H:R.14, H:R.201, H:R.240
- 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
AG
GB
BH
HC
CI
ID
DJ
JE
EK
KF
FL
L
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.20 Å
- Oligo State
- hetero-2-2-2-2-2-2-mer
- Ligands
- 2 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)
- 22 x SF4: IRON/SULFUR CLUSTER(Non-covalent)
- 6 x GOL: GLYCEROL(Non-functional Binders)
- 4 x 9S8: Non-cubane [4Fe-4S]-cluster(Non-covalent)
- 2 x COM: 1-THIOETHANESULFONIC ACID(Non-covalent)
- 1 x SO4: SULFATE ION(Non-functional Binders)
- 2 x FES: FE2/S2 (INORGANIC) CLUSTER(Non-covalent)
- 4 x ACT: ACETATE ION(Non-functional Binders)
- 2 x NFU: formyl[bis(hydrocyanato-1kappaC)]ironnickel(Fe-Ni)(Non-covalent)
- 4 x PE3: 3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL(Non-functional Binders)
- 3 x FE: FE (III) ION(Non-covalent)
- 1 x TP7: Coenzyme B
- 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
AG
GB
BH
HC
CI
ID
DJ
JE
EK
KF
FL
L