- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.06 Å
- Oligo State
- hetero-1-1-1-1-mer
- Ligands
- 1 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Covalent)
- 1 x Y3P: (~{Z})-2-oxidanylbut-2-enedioic acid(Non-covalent)
Y3P.2: 13 residues within 4Å:- Chain A: Q.61, G.62, F.130, H.253, L.263, T.265, E.266, R.297, H.364, R.408, G.410, A.411
- Ligands: FAD.1
13 PLIP interactions:13 interactions with chain A- Hydrophobic interactions: A:F.130
- Hydrogen bonds: A:G.62, A:H.253, A:T.265, A:E.266, A:R.297, A:R.297, A:A.411
- Salt bridges: A:H.253, A:R.297, A:R.297, A:H.364, A:R.408
- 1 x K: POTASSIUM ION(Non-covalent)
- 2 x AZI: AZIDE ION(Non-covalent)
AZI.4: 4 residues within 4Å:- Chain A: R.557, D.559, D.562, Y.563
7 PLIP interactions:7 interactions with chain A- Hydrogen bonds: A:R.557, A:R.557, A:D.559, A:Y.563
- Water bridges: A:R.557, A:D.559, A:D.559
AZI.75: 4 residues within 4Å:- Chain B: P.209, Y.213
- Chain D: A.6, H.9
1 PLIP interactions:1 interactions with chain D- Water bridges: D:Q.53
- 138 x UNL: UNKNOWN LIGAND(Covalent)(Non-covalent)(Non-functional Binders)
UNL.5: 4 residues within 4Å:- Chain A: Q.11, Y.12, V.450, A.451
Ligand excluded by PLIPUNL.6: 6 residues within 4Å:- Chain A: G.272, I.274, R.282, H.326, H.327, T.353
Ligand excluded by PLIPUNL.7: 5 residues within 4Å:- Chain A: I.346, F.347
- Chain B: P.42, M.43, K.88
Ligand excluded by PLIPUNL.8: 5 residues within 4Å:- Chain A: Y.98, K.375, A.423, T.427
- Ligands: UNL.16
Ligand excluded by PLIPUNL.9: 5 residues within 4Å:- Chain A: E.560, H.578, R.580, P.600, V.601
Ligand excluded by PLIPUNL.10: 6 residues within 4Å:- Chain A: S.165, L.166, Y.168, T.170, Y.172
- Chain B: K.123
Ligand excluded by PLIPUNL.11: 3 residues within 4Å:- Chain A: V.174, E.197
- Ligands: UNL.117
Ligand excluded by PLIPUNL.12: 6 residues within 4Å:- Chain A: H.227, R.469, E.521
- Chain B: R.63
- Ligands: UNL.27, UNL.69
Ligand excluded by PLIPUNL.13: 4 residues within 4Å:- Chain A: Y.287, S.620, Y.621
- Ligands: UNL.43
Ligand excluded by PLIPUNL.14: 5 residues within 4Å:- Chain A: E.121, E.122, G.123
- Chain B: S.145
- Ligands: UNL.103
Ligand excluded by PLIPUNL.15: 3 residues within 4Å:- Chain A: M.183, A.445, G.446
Ligand excluded by PLIPUNL.16: 4 residues within 4Å:- Chain A: Y.98, Q.102, R.422
- Ligands: UNL.8
Ligand excluded by PLIPUNL.17: 3 residues within 4Å:- Chain A: G.41, P.434
- Ligands: UNL.32
Ligand excluded by PLIPUNL.18: 8 residues within 4Å:- Chain A: F.177, A.178, L.179, D.232, M.236, R.239, N.527
- Ligands: UNL.26
Ligand excluded by PLIPUNL.19: 7 residues within 4Å:- Chain A: K.85, G.132, Q.133, Q.142, A.291, L.294, Y.621
Ligand excluded by PLIPUNL.20: 6 residues within 4Å:- Chain A: G.69, N.70, M.71, E.72, D.73, E.122
Ligand excluded by PLIPUNL.21: 5 residues within 4Å:- Chain A: E.72, D.73, L.135, Q.136
- Ligands: UNL.65
Ligand excluded by PLIPUNL.22: 5 residues within 4Å:- Chain A: K.49, T.228, E.521, E.524
- Chain B: R.63
Ligand excluded by PLIPUNL.23: 1 residues within 4Å:- Chain A: E.540
Ligand excluded by PLIPUNL.24: 2 residues within 4Å:- Chain A: Q.279, R.312
Ligand excluded by PLIPUNL.25: 2 residues within 4Å:- Chain A: Y.598
- Ligands: UNL.35
Ligand excluded by PLIPUNL.26: 5 residues within 4Å:- Chain A: L.179, D.180, R.239, N.452
- Ligands: UNL.18
Ligand excluded by PLIPUNL.27: 2 residues within 4Å:- Chain A: E.524
- Ligands: UNL.12
Ligand excluded by PLIPUNL.28: 4 residues within 4Å:- Chain A: T.305, P.361, V.482
- Ligands: UNL.29
Ligand excluded by PLIPUNL.29: 3 residues within 4Å:- Chain A: L.360, P.361
- Ligands: UNL.28
Ligand excluded by PLIPUNL.30: 2 residues within 4Å:- Chain A: D.351
- Ligands: UNL.31
Ligand excluded by PLIPUNL.31: 2 residues within 4Å:- Chain A: D.351
- Ligands: UNL.30
Ligand excluded by PLIPUNL.32: 4 residues within 4Å:- Chain A: A.40, P.434
- Ligands: UNL.17, UNL.41
Ligand excluded by PLIPUNL.33: 2 residues within 4Å:- Chain A: N.452
- Ligands: UNL.42
Ligand excluded by PLIPUNL.34: 3 residues within 4Å:- Chain A: K.474, Q.477, S.478
Ligand excluded by PLIPUNL.35: 4 residues within 4Å:- Chain A: E.576, K.581, Y.598
- Ligands: UNL.25
Ligand excluded by PLIPUNL.36: 2 residues within 4Å:- Chain A: E.72, L.135
Ligand excluded by PLIPUNL.37: 1 residues within 4Å:- Chain A: L.470
Ligand excluded by PLIPUNL.38: 1 residues within 4Å:- Chain A: K.543
Ligand excluded by PLIPUNL.39: 3 residues within 4Å:- Chain A: N.471, Q.498, I.499
Ligand excluded by PLIPUNL.40: 2 residues within 4Å:- Chain A: E.109
- Chain B: Q.137
Ligand excluded by PLIPUNL.41: 4 residues within 4Å:- Chain A: A.40, F.42, A.429
- Ligands: UNL.32
Ligand excluded by PLIPUNL.42: 3 residues within 4Å:- Chain A: Y.500, Q.526
- Ligands: UNL.33
Ligand excluded by PLIPUNL.43: 4 residues within 4Å:- Chain A: Y.287, S.620, Y.621
- Ligands: UNL.13
Ligand excluded by PLIPUNL.44: 3 residues within 4Å:- Chain A: K.474, T.475, K.495
Ligand excluded by PLIPUNL.45: 0 residues within 4Å:- (No contacts)
Ligand excluded by PLIPUNL.46: 2 residues within 4Å:- Chain A: T.120, E.121
Ligand excluded by PLIPUNL.47: 2 residues within 4Å:- Chain A: T.10, Q.11
Ligand excluded by PLIPUNL.48: 3 residues within 4Å:- Chain A: N.607, E.608, E.609
Ligand excluded by PLIPUNL.49: 1 residues within 4Å:- Chain A: E.467
Ligand excluded by PLIPUNL.50: 2 residues within 4Å:- Chain A: Y.81, K.85
Ligand excluded by PLIPUNL.51: 3 residues within 4Å:- Chain A: V.15, D.16
- Ligands: UNL.52
Ligand excluded by PLIPUNL.52: 2 residues within 4Å:- Chain A: V.14
- Ligands: UNL.51
Ligand excluded by PLIPUNL.53: 0 residues within 4Å:- (No contacts)
Ligand excluded by PLIPUNL.54: 1 residues within 4Å:- Chain A: G.349
Ligand excluded by PLIPUNL.55: 1 residues within 4Å:- Chain A: K.495
Ligand excluded by PLIPUNL.56: 1 residues within 4Å:- Chain A: Y.172
Ligand excluded by PLIPUNL.57: 0 residues within 4Å:- (No contacts)
Ligand excluded by PLIPUNL.58: 1 residues within 4Å:- Ligands: UNL.59
Ligand excluded by PLIPUNL.59: 3 residues within 4Å:- Chain A: F.137
- Ligands: UNL.58, UNL.60
Ligand excluded by PLIPUNL.60: 2 residues within 4Å:- Chain A: F.137
- Ligands: UNL.59
Ligand excluded by PLIPUNL.61: 4 residues within 4Å:- Chain A: T.170, Y.172
- Chain C: A.2, T.3
Ligand excluded by PLIPUNL.62: 1 residues within 4Å:- Chain A: E.101
Ligand excluded by PLIPUNL.63: 3 residues within 4Å:- Chain A: Y.563, K.565, L.567
Ligand excluded by PLIPUNL.64: 0 residues within 4Å:- (No contacts)
Ligand excluded by PLIPUNL.65: 1 residues within 4Å:- Ligands: UNL.21
Ligand excluded by PLIPUNL.66: 2 residues within 4Å:- Chain A: E.494, K.495
Ligand excluded by PLIPUNL.67: 1 residues within 4Å:- Chain A: E.430
Ligand excluded by PLIPUNL.68: 0 residues within 4Å:- (No contacts)
Ligand excluded by PLIPUNL.69: 4 residues within 4Å:- Chain A: R.469
- Chain B: I.49, N.53
- Ligands: UNL.12
Ligand excluded by PLIPUNL.70: 3 residues within 4Å:- Chain A: D.198, T.200, H.202
Ligand excluded by PLIPUNL.77: 3 residues within 4Å:- Chain B: T.244
- Chain C: D.109
- Ligands: UNL.82
Ligand excluded by PLIPUNL.78: 5 residues within 4Å:- Chain C: P.81, I.84, K.88, A.138, M.140
Ligand excluded by PLIPUNL.79: 5 residues within 4Å:- Chain B: S.194, D.196, T.199
- Ligands: NA.74, UNL.91
Ligand excluded by PLIPUNL.80: 2 residues within 4Å:- Chain A: R.167
- Chain B: E.134
Ligand excluded by PLIPUNL.81: 3 residues within 4Å:- Chain A: R.167
- Chain B: K.130, Y.198
Ligand excluded by PLIPUNL.82: 4 residues within 4Å:- Chain B: K.240, M.241, T.244
- Ligands: UNL.77
Ligand excluded by PLIPUNL.83: 1 residues within 4Å:- Chain B: Y.245
Ligand excluded by PLIPUNL.84: 2 residues within 4Å:- Chain B: D.176
- Ligands: UNL.124
Ligand excluded by PLIPUNL.85: 2 residues within 4Å:- Chain B: D.26
- Ligands: UNL.105
Ligand excluded by PLIPUNL.86: 3 residues within 4Å:- Chain A: R.218, H.227
- Chain B: R.66
Ligand excluded by PLIPUNL.87: 3 residues within 4Å:- Chain B: W.173, D.176
- Chain C: W.13
Ligand excluded by PLIPUNL.88: 4 residues within 4Å:- Chain B: R.62, S.72, A.74, P.113
Ligand excluded by PLIPUNL.89: 3 residues within 4Å:- Chain A: E.175
- Chain B: R.62, Y.119
Ligand excluded by PLIPUNL.90: 2 residues within 4Å:- Chain B: A.204, Q.205
Ligand excluded by PLIPUNL.91: 3 residues within 4Å:- Chain B: T.199
- Ligands: NA.74, UNL.79
Ligand excluded by PLIPUNL.92: 3 residues within 4Å:- Chain A: S.118, R.119
- Chain B: R.149
Ligand excluded by PLIPUNL.93: 2 residues within 4Å:- Chain B: D.153, L.155
Ligand excluded by PLIPUNL.94: 2 residues within 4Å:- Chain B: K.27
- Chain C: S.20
Ligand excluded by PLIPUNL.95: 2 residues within 4Å:- Chain B: D.20, D.26
Ligand excluded by PLIPUNL.96: 2 residues within 4Å:- Chain B: A.243
- Chain D: K.4
Ligand excluded by PLIPUNL.97: 1 residues within 4Å:- Ligands: UNL.148
Ligand excluded by PLIPUNL.98: 3 residues within 4Å:- Chain B: E.237, K.240
- Chain C: G.111
Ligand excluded by PLIPUNL.99: 1 residues within 4Å:- Ligands: UNL.108
Ligand excluded by PLIPUNL.100: 2 residues within 4Å:- Chain B: K.87, K.88
Ligand excluded by PLIPUNL.101: 2 residues within 4Å:- Chain B: E.140
- Ligands: UNL.108
Ligand excluded by PLIPUNL.102: 6 residues within 4Å:- Chain B: H.216, T.217, I.218
- Chain C: S.39, H.105
- Ligands: UNL.129
Ligand excluded by PLIPUNL.103: 2 residues within 4Å:- Chain B: S.145
- Ligands: UNL.14
Ligand excluded by PLIPUNL.104: 2 residues within 4Å:- Chain B: Q.31, T.32
Ligand excluded by PLIPUNL.105: 4 residues within 4Å:- Chain B: K.23, P.24, G.25
- Ligands: UNL.85
Ligand excluded by PLIPUNL.106: 2 residues within 4Å:- Chain B: S.124, E.126
Ligand excluded by PLIPUNL.107: 3 residues within 4Å:- Chain A: I.108
- Chain B: E.140, Q.141
Ligand excluded by PLIPUNL.108: 3 residues within 4Å:- Chain B: E.140
- Ligands: UNL.99, UNL.101
Ligand excluded by PLIPUNL.109: 4 residues within 4Å:- Chain A: P.116, T.160
- Chain B: R.189
- Ligands: UNL.110
Ligand excluded by PLIPUNL.110: 2 residues within 4Å:- Chain B: W.190
- Ligands: UNL.109
Ligand excluded by PLIPUNL.111: 1 residues within 4Å:- Chain B: M.30
Ligand excluded by PLIPUNL.112: 0 residues within 4Å:- (No contacts)
Ligand excluded by PLIPUNL.113: 2 residues within 4Å:- Chain B: K.130, E.201
Ligand excluded by PLIPUNL.114: 3 residues within 4Å:- Chain B: K.50, N.53, E.54
Ligand excluded by PLIPUNL.115: 1 residues within 4Å:- Chain B: Q.31
Ligand excluded by PLIPUNL.116: 1 residues within 4Å:- Chain B: R.223
Ligand excluded by PLIPUNL.117: 1 residues within 4Å:- Ligands: UNL.11
Ligand excluded by PLIPUNL.118: 2 residues within 4Å:- Chain B: G.41, D.46
Ligand excluded by PLIPUNL.119: 5 residues within 4Å:- Chain B: D.197, Y.198, T.199, E.200, E.201
Ligand excluded by PLIPUNL.123: 4 residues within 4Å:- Chain C: W.100, G.113, S.122, V.126
Ligand excluded by PLIPUNL.124: 3 residues within 4Å:- Chain C: A.10, W.13
- Ligands: UNL.84
Ligand excluded by PLIPUNL.125: 0 residues within 4Å:- (No contacts)
Ligand excluded by PLIPUNL.126: 1 residues within 4Å:- Chain C: A.87
Ligand excluded by PLIPUNL.127: 4 residues within 4Å:- Chain B: D.114, S.116
- Chain C: F.12, K.15
Ligand excluded by PLIPUNL.128: 2 residues within 4Å:- Chain C: P.22, L.23
Ligand excluded by PLIPUNL.129: 6 residues within 4Å:- Chain C: S.39, H.42, H.105
- Ligands: UNL.102, HEM.120, CBE.121
Ligand excluded by PLIPUNL.130: 1 residues within 4Å:- Chain C: L.116
Ligand excluded by PLIPUNL.131: 1 residues within 4Å:- Chain C: R.21
Ligand excluded by PLIPUNL.132: 2 residues within 4Å:- Chain C: K.75, S.78
Ligand excluded by PLIPUNL.133: 3 residues within 4Å:- Chain C: T.4, A.5, K.6
Ligand excluded by PLIPUNL.134: 2 residues within 4Å:- Chain B: K.123
- Chain C: E.8
Ligand excluded by PLIPUNL.135: 1 residues within 4Å:- Chain C: H.69
Ligand excluded by PLIPUNL.136: 0 residues within 4Å:- (No contacts)
Ligand excluded by PLIPUNL.137: 0 residues within 4Å:- (No contacts)
Ligand excluded by PLIPUNL.138: 0 residues within 4Å:- (No contacts)
Ligand excluded by PLIPUNL.139: 1 residues within 4Å:- Chain C: A.48
Ligand excluded by PLIPUNL.140: 1 residues within 4Å:- Chain C: M.38
Ligand excluded by PLIPUNL.141: 0 residues within 4Å:- (No contacts)
Ligand excluded by PLIPUNL.143: 4 residues within 4Å:- Chain C: M.140
- Chain D: V.97, W.101
- Ligands: UNL.144
Ligand excluded by PLIPUNL.144: 6 residues within 4Å:- Chain D: L.24, A.27, L.39, C.94, V.97
- Ligands: UNL.143
Ligand excluded by PLIPUNL.145: 2 residues within 4Å:- Chain B: W.173
- Chain D: Y.58
Ligand excluded by PLIPUNL.146: 5 residues within 4Å:- Chain C: S.50, S.54
- Chain D: T.44, H.48, S.76
Ligand excluded by PLIPUNL.147: 2 residues within 4Å:- Chain D: K.66, T.70
Ligand excluded by PLIPUNL.148: 3 residues within 4Å:- Chain D: Y.58, H.60
- Ligands: UNL.97
Ligand excluded by PLIPUNL.149: 0 residues within 4Å:- (No contacts)
Ligand excluded by PLIPUNL.150: 2 residues within 4Å:- Chain D: D.62
- Ligands: UNL.151
Ligand excluded by PLIPUNL.151: 1 residues within 4Å:- Ligands: UNL.150
Ligand excluded by PLIPUNL.152: 1 residues within 4Å:- Chain D: S.38
Ligand excluded by PLIP- 1 x FES: FE2/S2 (INORGANIC) CLUSTER(Non-covalent)
- 1 x SF4: IRON/SULFUR CLUSTER(Non-covalent)
- 1 x F3S: FE3-S4 CLUSTER(Non-covalent)
- 1 x NA: SODIUM ION(Non-functional Binders)
- 1 x GOL: GLYCEROL(Non-functional Binders)
- 1 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)
HEM.120: 19 residues within 4Å:- Chain B: H.216
- Chain C: H.42, R.43, G.46, V.47, L.49, S.50, H.98, T.99, G.102, H.105
- Chain D: R.14, S.17, L.20, L.43, H.46, G.50, L.51
- Ligands: UNL.129
17 PLIP interactions:6 interactions with chain D, 2 interactions with chain B, 9 interactions with chain C,- Hydrophobic interactions: D:L.20, D:L.43, D:L.51, C:L.49, C:L.49, C:H.105
- Hydrogen bonds: D:R.14, D:G.50
- Metal complexes: D:H.46, C:H.98
- Water bridges: B:H.216, C:H.105, C:H.105
- Salt bridges: B:H.216, C:R.43, C:H.105
- pi-Stacking: C:H.42
- 1 x CBE: 2-METHYL-N-PHENYL-5,6-DIHYDRO-1,4-OXATHIINE-3-CARBOXAMIDE(Non-covalent)
- 2 x BOG: octyl beta-D-glucopyranoside(Non-covalent)
BOG.122: 7 residues within 4Å:- Chain B: R.223
- Chain C: K.31, W.32, S.33, L.34, P.35, E.120
5 PLIP interactions:3 interactions with chain C, 2 interactions with chain B- Hydrogen bonds: C:K.31, C:L.34, C:E.120, B:R.223, B:R.223
BOG.142: 7 residues within 4Å:- Chain D: H.9, L.45, H.48, W.49, N.69, Y.73, S.76
6 PLIP interactions:6 interactions with chain D- Hydrophobic interactions: D:L.45, D:Y.73
- Hydrogen bonds: D:H.9, D:W.49, D:N.69
- Salt bridges: D:H.48
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Huang, L.S. et al., 3-nitropropionic acid is a suicide inhibitor of mitochondrial respiration that, upon oxidation by complex II, forms a covalent adduct with a catalytic base arginine in the active site of the enzyme. J.Biol.Chem. (2006)
- Release Date
- 2005-12-20
- Peptides
- Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial: A
Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial: B
Succinate dehydrogenase cytochrome b560 subunit, mitochondrial: C
Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial: D - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
CD
D - Membrane
-
We predict this structure to be a membrane protein.
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.06 Å
- Oligo State
- hetero-1-1-1-1-mer
- Ligands
- 1 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Covalent)
- 1 x Y3P: (~{Z})-2-oxidanylbut-2-enedioic acid(Non-covalent)
- 1 x K: POTASSIUM ION(Non-covalent)
- 2 x AZI: AZIDE ION(Non-covalent)
- 138 x UNL: UNKNOWN LIGAND(Covalent)(Non-covalent)(Non-functional Binders)
- 1 x FES: FE2/S2 (INORGANIC) CLUSTER(Non-covalent)
- 1 x SF4: IRON/SULFUR CLUSTER(Non-covalent)
- 1 x F3S: FE3-S4 CLUSTER(Non-covalent)
- 1 x NA: SODIUM ION(Non-functional Binders)
- 1 x GOL: GLYCEROL(Non-functional Binders)
- 1 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)
- 1 x CBE: 2-METHYL-N-PHENYL-5,6-DIHYDRO-1,4-OXATHIINE-3-CARBOXAMIDE(Non-covalent)
- 2 x BOG: octyl beta-D-glucopyranoside(Non-covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Huang, L.S. et al., 3-nitropropionic acid is a suicide inhibitor of mitochondrial respiration that, upon oxidation by complex II, forms a covalent adduct with a catalytic base arginine in the active site of the enzyme. J.Biol.Chem. (2006)
- Release Date
- 2005-12-20
- Peptides
- Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial: A
Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial: B
Succinate dehydrogenase cytochrome b560 subunit, mitochondrial: C
Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial: D - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
CD
D - Membrane
-
We predict this structure to be a membrane protein.