- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.20 Å
- Oligo State
- hetero-2-2-2-2-2-2-mer
- Ligands
- 22 x SF4: IRON/SULFUR CLUSTER(Non-covalent)
- 6 x GOL: GLYCEROL(Non-functional Binders)
GOL.7: 5 residues within 4Å:- Chain A: V.337, E.339, E.340
- Chain H: E.168
- Chain I: E.85
4 PLIP interactions:1 interactions with chain I, 2 interactions with chain A, 1 interactions with chain H- Hydrogen bonds: I:E.85, A:V.337, A:E.339, H:E.168
GOL.13: 6 residues within 4Å:- Chain B: R.201, F.233
- Chain C: T.117, A.127, V.128
- Ligands: GOL.14
1 PLIP interactions:1 interactions with chain B- Hydrogen bonds: B:R.201
GOL.14: 4 residues within 4Å:- Chain B: R.201, L.236
- Chain C: V.128
- Ligands: GOL.13
2 PLIP interactions:2 interactions with chain B- Hydrogen bonds: B:R.201
- Water bridges: B:R.14
GOL.22: 6 residues within 4Å:- Chain E: L.22, L.29, N.32, A.157, K.161, L.164
3 PLIP interactions:3 interactions with chain E- Hydrogen bonds: E:E.25, E:E.25, E:N.32
GOL.33: 7 residues within 4Å:- Chain G: Y.427, Y.441, F.452, L.477
- Chain I: C.34, Y.35, Q.36
4 PLIP interactions:2 interactions with chain I, 2 interactions with chain G- Hydrogen bonds: I:C.34, G:Y.427
- Water bridges: I:R.59, G:F.452
GOL.48: 3 residues within 4Å:- Chain K: S.137, V.142, F.145
2 PLIP interactions:2 interactions with chain K- Hydrogen bonds: K:S.137, K:V.142
- 4 x PE3: 3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL(Non-functional Binders)
PE3.8: 8 residues within 4Å:- Chain A: Q.144, M.165, G.166, F.167, A.566
- Chain G: M.165, F.167, A.566
No protein-ligand interaction detected (PLIP)PE3.23: 8 residues within 4Å:- Chain F: L.206, E.207, K.210, E.312, F.313, F.317, L.326, Y.329
3 PLIP interactions:3 interactions with chain F- Hydrophobic interactions: F:E.312, F:Y.329
- Hydrogen bonds: F:K.210
PE3.24: 5 residues within 4Å:- Chain F: H.136, I.139, K.197, K.204, L.205
No protein-ligand interaction detected (PLIP)PE3.49: 7 residues within 4Å:- Chain L: K.203, L.206, E.207, K.210, F.317, L.326, Y.329
1 PLIP interactions:1 interactions with chain L- Hydrogen bonds: L:K.210
- 2 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)
FAD.9: 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, L.353, E.356, V.402, 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:E.356, A:V.402, A:Y.406
- Hydrogen bonds: A:G.151, A:A.154, A:K.174, A:G.180, 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:T.175, A:E.219, A:C.541, A:C.541
FAD.37: 36 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, K.187, T.188, F.189, A.327, I.328, G.329, Y.330, A.352, L.353, E.356, V.402, Y.406, K.409, S.500, V.504, G.539, A.540, K.545, D.546, I.547, P.548, S.550
35 PLIP interactions:35 interactions with chain G- Hydrophobic interactions: G:L.185, G:Y.330, G:A.352, G:E.356, G:V.402, G:Y.406, G:Y.406
- Hydrogen bonds: G:G.151, 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:V.153, G:V.153, G:E.173, G:T.175, G:R.181, G:G.329, G:Y.330, G:C.541
- pi-Stacking: G:F.189
- 4 x 9S8: Non-cubane [4Fe-4S]-cluster(Non-covalent)
9S8.10: 11 residues within 4Å:- Chain B: G.8, C.9, I.10, 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
9S8.11: 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
6 PLIP interactions:6 interactions with chain B,- Metal complexes: B:C.153, B:C.193, B:C.194, B:C.231, B:C.234, B:C.234
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
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
9S8.39: 11 residues within 4Å:- Chain H: H.150, G.152, C.153, H.154, C.193, C.194, C.231, F.233, C.234
- Chain I: T.78
- Ligands: COM.40
6 PLIP interactions:6 interactions with chain H,- Metal complexes: H:C.153, H:C.193, H:C.194, H:C.231, H:C.234, 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, G.197, G.198, G.199, C.231, F.233
- Ligands: 9S8.11
4 PLIP interactions:3 interactions with chain B, 1 interactions with chain C- Hydrogen bonds: B:G.46, B:G.198, B:G.199
- Water bridges: C:T.79
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
6 PLIP interactions:6 interactions with chain H- Hydrogen bonds: H:A.44, H:G.46, H:V.47, H:G.198
- Water bridges: H:G.199
- Salt bridges: H:H.154
- 2 x FES: FE2/S2 (INORGANIC) CLUSTER(Non-covalent)
FES.17: 10 residues within 4Å:- Chain D: C.13, W.15, M.41, C.42, S.43, G.66, C.67, C.72, H.73, Y.74
4 PLIP interactions:4 interactions with chain D,- Metal complexes: D:C.13, D:C.42, D:C.67, D:C.72
FES.44: 10 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
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)
- 2 x NFU: formyl[bis(hydrocyanato-1kappaC)]ironnickel(Fe-Ni)(Non-covalent)
NFU.25: 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.50: 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:T.399, L:C.442
- Metal complexes: L:C.61, L:C.64, L:C.64, L:C.442, L:C.445, L:C.445
- 3 x FE: FE (III) ION(Non-covalent)
FE.26: 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.9, H2O.10, H2O.11
FE.34: 4 residues within 4Å:- Chain A: C.197
- Chain G: C.46, H.76
- Ligands: SF4.27
2 PLIP interactions:2 interactions with chain G- Metal complexes: G:C.46, G:H.76
FE.51: 5 residues within 4Å:- Chain L: E.42, K.273, N.394, 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.21, H2O.21, H2O.23
- 2 x ACT: ACETATE ION(Non-functional Binders)
- 1 x TP7: Coenzyme B
TP7.41: 10 residues within 4Å:- Chain H: R.14, A.44, R.201, A.202, F.233, R.240
- Chain I: T.117, V.128
- Ligands: 9S8.38, COM.40
7 PLIP interactions:5 interactions with chain H, 2 interactions with chain I- Hydrophobic interactions: H:F.233, I:T.117, I:V.128
- Hydrogen bonds: H:R.201
- 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
- 22 x SF4: IRON/SULFUR CLUSTER(Non-covalent)
- 6 x GOL: GLYCEROL(Non-functional Binders)
- 4 x PE3: 3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL(Non-functional Binders)
- 2 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)
- 4 x 9S8: Non-cubane [4Fe-4S]-cluster(Non-covalent)
- 2 x COM: 1-THIOETHANESULFONIC ACID(Non-covalent)
- 2 x FES: FE2/S2 (INORGANIC) CLUSTER(Non-covalent)
- 1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)
- 2 x NFU: formyl[bis(hydrocyanato-1kappaC)]ironnickel(Fe-Ni)(Non-covalent)
- 3 x FE: FE (III) ION(Non-covalent)
- 2 x ACT: ACETATE ION(Non-functional Binders)
- 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