SMTL ID : 2fbw.2 (1 other biounit)

Avian respiratory complex II with carboxin bound

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)

FAD.1: 38 residues within 4Å: Chain A: V.24, G.25, A.26, G.27, G.28, A.29, V.47, T.48, K.49, L.50, S.55, H.56, T.57, A.59, A.60, Q.61, G.62, G.63, Y.176, F.177, A.178, A.212, T.213, G.214, T.224, D.232, L.263, H.364, Y.365, G.396, E.397, R.408, A.411, N.412, S.413, L.414, L.417 Ligands: Y3P.2 37 PLIP interactions: 37 interactions with chain A Hydrophobic interactions: A:A.59, A:L.263, A:L.263 Hydrogen bonds: A:A.26, A:A.26, A:G.28, A:A.29, A:T.48, A:K.49, A:K.49, A:L.50, A:H.56, A:T.57, A:T.57, A:Q.61, A:G.62, A:G.63, A:G.63, A:A.178, A:A.178, A:G.214, A:E.397, A:E.397, A:R.408, A:R.408, A:A.411, A:S.413, A:S.413, A:L.414 Water bridges: A:G.27, A:G.27, A:G.215, A:E.397, A:E.397, A:A.398, A:N.527 pi-Cation interactions: A:H.364

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)

K.3: 6 residues within 4Å: Chain A: Y.365, N.366, M.367, G.368, E.397, A.399 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:N.366, A:G.368, A:E.397, A:A.399

1 x AZI: AZIDE ION(Non-covalent)

AZI.4: 4 residues within 4Å: Chain A: R.557, D.559, F.561, Y.563 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:R.557, A:R.557, A:D.559, A:F.561, A:Y.563 Water bridges: A:R.557, A:D.559, A:D.559

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 5 residues within 4Å: Chain A: R.32, G.36, E.39, A.40, R.422 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.32, A:R.32, A:R.422

118 x UNL: UNKNOWN LIGAND(Non-functional Binders)(Non-covalent)

UNL.6: 1 residues within 4Å: Chain A: R.286 Ligand excluded by PLIP UNL.7: 3 residues within 4Å: Chain A: T.305, R.309 Ligands: UNL.48 Ligand excluded by PLIP UNL.8: 3 residues within 4Å: Chain A: E.101, L.606, N.607 Ligand excluded by PLIP UNL.9: 7 residues within 4Å: Chain A: S.222, G.256, I.257, G.261, L.360, T.362 Ligands: UNL.53 Ligand excluded by PLIP UNL.10: 1 residues within 4Å: Chain A: Q.11 Ligand excluded by PLIP UNL.11: 11 residues within 4Å: Chain A: T.170, S.171, Y.172, V.174, Y.176 Chain C: A.2, T.3, E.8 Ligands: UNL.19, UNL.54, UNL.98 Ligand excluded by PLIP UNL.12: 1 residues within 4Å: Chain A: K.139 Ligand excluded by PLIP UNL.13: 2 residues within 4Å: Chain A: D.180, R.239 Ligand excluded by PLIP UNL.14: 3 residues within 4Å: Chain A: T.10, Q.11, V.450 Ligand excluded by PLIP UNL.15: 2 residues within 4Å: Chain A: D.20, E.436 Ligand excluded by PLIP UNL.16: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNL.17: 2 residues within 4Å: Chain A: Q.332 Ligands: UNL.94 Ligand excluded by PLIP UNL.18: 4 residues within 4Å: Chain A: D.16, H.17, E.18, F.19 Ligand excluded by PLIP UNL.19: 5 residues within 4Å: Chain A: Y.162 Chain C: E.8 Ligands: UNL.11, UNL.54, UNL.57 Ligand excluded by PLIP UNL.20: 3 residues within 4Å: Chain A: E.281, R.286, R.312 Ligand excluded by PLIP UNL.21: 3 residues within 4Å: Chain A: K.474, T.475, K.495 Ligand excluded by PLIP UNL.22: 1 residues within 4Å: Chain A: N.373 Ligand excluded by PLIP UNL.23: 3 residues within 4Å: Chain A: Q.324, H.327 Ligands: UNL.50 Ligand excluded by PLIP UNL.24: 4 residues within 4Å: Chain A: H.227, R.469, E.521 Chain B: R.63 Ligand excluded by PLIP UNL.25: 3 residues within 4Å: Chain A: N.471, I.499, D.502 Ligand excluded by PLIP UNL.26: 5 residues within 4Å: Chain A: D.510 Chain B: R.18, D.20, T.58, K.109 Ligand excluded by PLIP UNL.27: 7 residues within 4Å: Chain A: E.560, K.572, H.578, R.580, P.600, V.601, D.603 Ligand excluded by PLIP UNL.28: 3 residues within 4Å: Chain A: Y.98, Y.374, T.427 Ligand excluded by PLIP UNL.29: 2 residues within 4Å: Chain A: F.347 Chain B: P.42 Ligand excluded by PLIP UNL.30: 1 residues within 4Å: Chain A: D.16 Ligand excluded by PLIP UNL.31: 6 residues within 4Å: Chain A: G.69, E.72, D.73, E.122, K.124 Ligands: UNL.69 Ligand excluded by PLIP UNL.32: 3 residues within 4Å: Chain A: M.71, E.72, H.144 Ligand excluded by PLIP UNL.33: 4 residues within 4Å: Chain A: F.221, K.474, Q.477, S.478 Ligand excluded by PLIP UNL.34: 4 residues within 4Å: Chain A: Y.500, L.503, Q.526 Ligands: UNL.46 Ligand excluded by PLIP UNL.35: 2 residues within 4Å: Chain A: N.75, W.76 Ligand excluded by PLIP UNL.36: 4 residues within 4Å: Chain A: F.177, L.179, R.239, L.523 Ligand excluded by PLIP UNL.37: 5 residues within 4Å: Chain A: A.106, E.109, V.418, V.419, R.422 Ligand excluded by PLIP UNL.38: 2 residues within 4Å: Chain A: D.386, I.602 Ligand excluded by PLIP UNL.39: 4 residues within 4Å: Chain A: E.576, H.578, W.579, K.581 Ligand excluded by PLIP UNL.40: 2 residues within 4Å: Chain A: M.183, A.240 Ligand excluded by PLIP UNL.41: 2 residues within 4Å: Chain A: Y.258, G.259 Ligand excluded by PLIP UNL.42: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNL.43: 3 residues within 4Å: Chain A: A.481, V.482 Ligands: UNL.48 Ligand excluded by PLIP UNL.44: 1 residues within 4Å: Chain A: R.77 Ligand excluded by PLIP UNL.45: 1 residues within 4Å: Chain A: R.511 Ligand excluded by PLIP UNL.46: 2 residues within 4Å: Chain A: L.503 Ligands: UNL.34 Ligand excluded by PLIP UNL.47: 1 residues within 4Å: Chain A: E.121 Ligand excluded by PLIP UNL.48: 5 residues within 4Å: Chain A: A.481, V.482, F.483 Ligands: UNL.7, UNL.43 Ligand excluded by PLIP UNL.49: 2 residues within 4Å: Chain A: K.593, V.594 Ligand excluded by PLIP UNL.50: 3 residues within 4Å: Chain A: G.280 Ligands: UNL.23, UNL.51 Ligand excluded by PLIP UNL.51: 2 residues within 4Å: Chain A: G.280 Ligands: UNL.50 Ligand excluded by PLIP UNL.52: 1 residues within 4Å: Chain A: Y.258 Ligand excluded by PLIP UNL.53: 4 residues within 4Å: Chain A: Y.258, G.259, L.360 Ligands: UNL.9 Ligand excluded by PLIP UNL.54: 3 residues within 4Å: Chain A: F.51 Ligands: UNL.11, UNL.19 Ligand excluded by PLIP UNL.55: 3 residues within 4Å: Chain A: R.309, F.483, E.552 Ligand excluded by PLIP UNL.56: 1 residues within 4Å: Chain A: R.167 Ligand excluded by PLIP UNL.57: 5 residues within 4Å: Chain A: P.52, Y.162, S.165, Y.172 Ligands: UNL.19 Ligand excluded by PLIP UNL.58: 2 residues within 4Å: Chain A: E.491, E.494 Ligand excluded by PLIP UNL.59: 4 residues within 4Å: Chain A: R.302, V.482, A.548, A.550 Ligand excluded by PLIP UNL.60: 2 residues within 4Å: Chain A: G.41, P.434 Ligand excluded by PLIP UNL.61: 2 residues within 4Å: Chain A: F.575, E.576 Ligand excluded by PLIP UNL.62: 1 residues within 4Å: Chain A: T.353 Ligand excluded by PLIP UNL.63: 1 residues within 4Å: Chain A: E.540 Ligand excluded by PLIP UNL.64: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNL.65: 1 residues within 4Å: Chain A: E.577 Ligand excluded by PLIP UNL.66: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNL.67: 4 residues within 4Å: Chain A: V.15, D.198, T.200, H.202 Ligand excluded by PLIP UNL.68: 1 residues within 4Å: Chain A: F.137 Ligand excluded by PLIP UNL.69: 1 residues within 4Å: Ligands: UNL.31 Ligand excluded by PLIP UNL.73: 4 residues within 4Å: Chain B: D.176 Chain C: M.9, A.10, W.13 Ligand excluded by PLIP UNL.74: 3 residues within 4Å: Chain B: T.244 Chain C: D.109 Ligands: UNL.82 Ligand excluded by PLIP UNL.75: 8 residues within 4Å: Chain B: H.104, M.105, Y.106, Y.171, G.175 Chain C: F.12, W.13, L.23 Ligand excluded by PLIP UNL.76: 2 residues within 4Å: Chain B: D.176 Chain C: W.13 Ligand excluded by PLIP UNL.77: 3 residues within 4Å: Chain B: S.194, D.196, T.199 Ligand excluded by PLIP UNL.78: 3 residues within 4Å: Chain B: T.8, R.10, N.38 Ligand excluded by PLIP UNL.79: 5 residues within 4Å: Chain B: I.125, E.126, K.130, R.202, Q.205 Ligand excluded by PLIP UNL.80: 5 residues within 4Å: Chain A: R.164, R.167, Y.168 Chain B: E.134, Q.137 Ligand excluded by PLIP UNL.81: 1 residues within 4Å: Chain B: D.22 Ligand excluded by PLIP UNL.82: 1 residues within 4Å: Ligands: UNL.74 Ligand excluded by PLIP UNL.83: 6 residues within 4Å: Chain A: K.49, T.228, T.517, E.521, E.524 Chain B: R.63 Ligand excluded by PLIP UNL.84: 4 residues within 4Å: Chain B: I.49, K.50, N.53, E.54 Ligand excluded by PLIP UNL.85: 2 residues within 4Å: Chain B: T.199, Y.245 Ligand excluded by PLIP UNL.86: 2 residues within 4Å: Chain B: P.42, I.89 Ligand excluded by PLIP UNL.87: 3 residues within 4Å: Chain B: A.78, D.90, T.97 Ligand excluded by PLIP UNL.88: 3 residues within 4Å: Chain A: I.108 Chain B: E.140, Q.141 Ligand excluded by PLIP UNL.89: 3 residues within 4Å: Chain A: H.155, H.159 Chain B: Y.156 Ligand excluded by PLIP UNL.90: 4 residues within 4Å: Chain B: Y.213, C.215, K.239 Chain D: W.10 Ligand excluded by PLIP UNL.91: 1 residues within 4Å: Chain B: E.126 Ligand excluded by PLIP UNL.92: 2 residues within 4Å: Chain A: E.109 Chain B: G.138 Ligand excluded by PLIP UNL.93: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNL.94: 1 residues within 4Å: Ligands: UNL.17 Ligand excluded by PLIP UNL.95: 2 residues within 4Å: Chain B: K.131, Y.142 Ligand excluded by PLIP UNL.96: 2 residues within 4Å: Chain B: K.27 Chain C: S.20 Ligand excluded by PLIP UNL.97: 2 residues within 4Å: Chain B: I.89, P.91 Ligand excluded by PLIP UNL.98: 2 residues within 4Å: Ligands: UNL.11, UNL.99 Ligand excluded by PLIP UNL.99: 2 residues within 4Å: Chain B: Y.119 Ligands: UNL.98 Ligand excluded by PLIP UNL.100: 5 residues within 4Å: Chain B: N.174, D.176, K.177, F.210 Chain D: H.60 Ligand excluded by PLIP UNL.101: 3 residues within 4Å: Chain A: R.218, F.221 Chain B: R.66 Ligand excluded by PLIP UNL.102: 3 residues within 4Å: Chain B: L.83, T.86, P.226 Ligand excluded by PLIP UNL.103: 3 residues within 4Å: Chain B: K.13, T.32, E.34 Ligand excluded by PLIP UNL.104: 3 residues within 4Å: Chain B: K.13, T.96 Ligands: UNL.105 Ligand excluded by PLIP UNL.105: 2 residues within 4Å: Chain B: T.32 Ligands: UNL.104 Ligand excluded by PLIP UNL.106: 3 residues within 4Å: Chain A: A.105 Chain B: G.138, K.139 Ligand excluded by PLIP UNL.107: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNL.108: 1 residues within 4Å: Chain B: Q.150 Ligand excluded by PLIP UNL.113: 5 residues within 4Å: Chain C: W.100, I.103, G.113, S.122, L.129 Ligand excluded by PLIP UNL.114: 2 residues within 4Å: Chain C: Y.85, A.139 Ligand excluded by PLIP UNL.115: 4 residues within 4Å: Chain B: N.220, R.223, T.224 Chain C: Y.30 Ligand excluded by PLIP UNL.116: 7 residues within 4Å: Chain C: L.49, L.91, P.94, I.137 Chain D: V.97 Ligands: UNL.120, UNL.127 Ligand excluded by PLIP UNL.117: 1 residues within 4Å: Chain C: Q.121 Ligand excluded by PLIP UNL.118: 1 residues within 4Å: Chain C: R.21 Ligand excluded by PLIP UNL.119: 1 residues within 4Å: Chain C: S.28 Ligand excluded by PLIP UNL.120: 2 residues within 4Å: Chain C: A.48 Ligands: UNL.116 Ligand excluded by PLIP UNL.121: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNL.122: 2 residues within 4Å: Chain D: P.33, Y.88 Ligand excluded by PLIP UNL.123: 5 residues within 4Å: Chain D: L.45, H.48, W.49, N.69, Y.73 Ligand excluded by PLIP UNL.124: 2 residues within 4Å: Chain D: Y.58, H.60 Ligand excluded by PLIP UNL.125: 3 residues within 4Å: Chain B: W.173 Chain C: H.26 Chain D: Y.58 Ligand excluded by PLIP UNL.126: 4 residues within 4Å: Chain D: H.9, W.10, E.13, Q.53 Ligand excluded by PLIP UNL.127: 7 residues within 4Å: Chain D: A.27, Y.28, P.31, L.39, C.94, A.98 Ligands: UNL.116 Ligand excluded by PLIP UNL.128: 9 residues within 4Å: Chain C: S.50, S.54 Chain D: L.43, T.44, G.47, H.48, L.51, L.75, S.76 Ligand excluded by PLIP UNL.129: 1 residues within 4Å: Chain D: S.12 Ligand excluded by PLIP UNL.130: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP

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

FES.70: 11 residues within 4Å: Chain B: R.63, S.64, C.65, R.66, G.68, I.69, C.70, G.71, S.72, C.73, C.85 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.65, B:C.70, B:C.73, B:C.85

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

SF4.71: 11 residues within 4Å: Chain B: C.158, I.159, L.160, C.161, A.162, C.163, C.164, A.182, M.185, C.225, P.226 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.158, B:C.161, B:C.164, B:C.225

1 x F3S: FE3-S4 CLUSTER(Non-covalent)

F3S.72: 11 residues within 4Å: Chain B: C.168, Y.178, P.181, C.215, H.216, T.217, I.218, M.219, N.220, C.221, I.235 3 PLIP interactions: 3 interactions with chain B, Metal complexes: B:C.168, B:C.215, B:C.221

1 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)

HEM.109: 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, Q.53 18 PLIP interactions: 8 interactions with chain D, 8 interactions with chain C, 2 interactions with chain B, Hydrophobic interactions: D:L.20, D:L.43, D:L.51, C:L.49, C:L.49, C:H.105 Hydrogen bonds: D:G.50 Water bridges: D:R.14, D:R.14, C:H.105, B:H.216 Salt bridges: D:R.14, C:R.43, C:H.105, B:H.216 Metal complexes: D:H.46, C:H.98 pi-Stacking: C:H.42

1 x CBE: 2-METHYL-N-PHENYL-5,6-DIHYDRO-1,4-OXATHIINE-3-CARBOXAMIDE(Non-covalent)

CBE.110: 12 residues within 4Å: Chain B: P.169, S.170, W.173, H.216, I.218 Chain C: I.27, W.32, S.39, I.40, R.43 Chain D: D.57, Y.58 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain C Hydrophobic interactions: B:P.169, B:W.173, C:I.27, C:W.32, C:I.40

1 x UMQ: UNDECYL-MALTOSIDE(Non-covalent)

UMQ.111: 9 residues within 4Å: Chain B: R.223 Chain C: K.31, W.32, S.33, L.34, P.35, A.37, E.120 Ligands: BOG.112 10 PLIP interactions: 7 interactions with chain C, 3 interactions with chain B Hydrophobic interactions: C:A.37 Hydrogen bonds: C:K.31, C:K.31, C:L.34, C:E.120, C:E.120, B:R.223, B:R.223 Water bridges: C:K.31 Salt bridges: B:R.223

1 x BOG: octyl beta-D-glucopyranoside(Non-covalent)

BOG.112: 4 residues within 4Å: Chain C: L.34, E.120, V.124 Ligands: UMQ.111 No protein-ligand interaction detected (PLIP)

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
N

B
O

C
P

D
Q

Membrane

We predict this structure to be a membrane protein.
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Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial

Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial

Succinate dehydrogenase cytochrome b560 subunit, mitochondrial

Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial

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