SMTL ID : 2h88.4 (3 other biounits)

Avian Mitochondrial Respiratory Complex II at 1.8 Angstrom Resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.74 Å

Oligo State

hetero-1-2-2-2-mer

Ligands

3 x K: POTASSIUM ION(Non-covalent)

K.1: 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 K.11: 4 residues within 4Å: Chain B: M.191, D.193, D.196, T.199 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:M.191, B:D.193, H2O.24, H2O.26 K.42: 4 residues within 4Å: Chain E: M.191, D.193, D.196, T.199 4 PLIP interactions: 3 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:M.191, E:D.193, E:D.196, H2O.41

1 x AZI: AZIDE ION(Non-covalent)

AZI.2: 3 residues within 4Å: Chain A: R.218, F.221, H.227 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.218, A:R.218, A:F.221, A:H.227

1 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Covalent)

FAD.3: 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: TEO.4 33 PLIP interactions: 33 interactions with chain A Hydrophobic interactions: A:A.59, A:L.263, A:L.263 Hydrogen bonds: A:A.26, A:A.26, A:A.29, A:K.49, A:K.49, A:L.50, A:H.56, A:T.57, A:T.57, A:Q.61, A:G.63, A:G.63, A:A.178, A:A.178, A:G.214, A:D.232, 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.30, A:G.215, A:E.397, A:E.397, A:A.398 pi-Cation interactions: A:H.364

1 x TEO: MALATE LIKE INTERMEDIATE(Non-covalent)

TEO.4: 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.3 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:F.130 Hydrogen bonds: A:G.62, A:H.253, A:E.266, A:R.297, A:A.411 Salt bridges: A:H.253, A:R.297, A:R.297, A:H.364, A:R.408

54 x UNL: UNKNOWN LIGAND(Non-functional Binders)

UNL.5: 1 residues within 4Å: Chain A: E.101 Ligand excluded by PLIP UNL.6: 3 residues within 4Å: Chain A: Q.498, D.502 Ligands: UNL.7 Ligand excluded by PLIP UNL.7: 4 residues within 4Å: Chain A: Q.498, D.502 Ligands: UNL.6, UNL.8 Ligand excluded by PLIP UNL.8: 2 residues within 4Å: Ligands: UNL.7, UNL.9 Ligand excluded by PLIP UNL.9: 2 residues within 4Å: Ligands: UNL.8, UNL.10 Ligand excluded by PLIP UNL.10: 1 residues within 4Å: Ligands: UNL.9 Ligand excluded by PLIP UNL.15: 4 residues within 4Å: Chain B: W.173 Chain D: Y.58 Ligands: UNL.16, UNL.22 Ligand excluded by PLIP UNL.16: 5 residues within 4Å: Chain B: I.218 Chain D: Y.58 Ligands: UNL.15, UNL.17, UNL.22 Ligand excluded by PLIP UNL.17: 3 residues within 4Å: Chain B: H.216, I.218 Ligands: UNL.16 Ligand excluded by PLIP UNL.18: 3 residues within 4Å: Chain B: K.39, K.50, E.54 Ligand excluded by PLIP UNL.22: 5 residues within 4Å: Chain B: P.169 Chain C: I.40 Ligands: UNL.15, UNL.16, UNL.23 Ligand excluded by PLIP UNL.23: 3 residues within 4Å: Chain B: P.169 Chain C: I.40 Ligands: UNL.22 Ligand excluded by PLIP UNL.24: 3 residues within 4Å: Chain C: L.91, L.95 Ligands: UNL.36 Ligand excluded by PLIP UNL.25: 4 residues within 4Å: Chain C: F.56 Chain D: V.97 Ligands: UNL.27, UNL.36 Ligand excluded by PLIP UNL.26: 1 residues within 4Å: Chain C: S.96 Ligand excluded by PLIP UNL.27: 2 residues within 4Å: Chain C: F.56 Ligands: UNL.25 Ligand excluded by PLIP UNL.28: 5 residues within 4Å: Chain C: S.50, S.54 Chain D: L.43, G.47 Ligands: UNL.39 Ligand excluded by PLIP UNL.29: 2 residues within 4Å: Chain C: T.41 Ligands: UNL.32 Ligand excluded by PLIP UNL.30: 2 residues within 4Å: Chain C: S.28, I.29 Ligand excluded by PLIP UNL.31: 1 residues within 4Å: Chain C: I.40 Ligand excluded by PLIP UNL.32: 1 residues within 4Å: Ligands: UNL.29 Ligand excluded by PLIP UNL.33: 3 residues within 4Å: Chain C: K.18, S.19, S.20 Ligand excluded by PLIP UNL.34: 1 residues within 4Å: Chain C: V.107 Ligand excluded by PLIP UNL.35: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNL.36: 4 residues within 4Å: Chain C: V.53 Chain D: L.24 Ligands: UNL.24, UNL.25 Ligand excluded by PLIP UNL.37: 2 residues within 4Å: Chain D: V.97, W.101 Ligand excluded by PLIP UNL.38: 1 residues within 4Å: Ligands: UNL.41 Ligand excluded by PLIP UNL.39: 4 residues within 4Å: Chain D: T.44, H.48, S.76 Ligands: UNL.28 Ligand excluded by PLIP UNL.40: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNL.41: 2 residues within 4Å: Chain D: G.71 Ligands: UNL.38 Ligand excluded by PLIP UNL.46: 5 residues within 4Å: Chain E: P.169, W.173 Chain G: Y.58 Ligands: UNL.47, UNL.53 Ligand excluded by PLIP UNL.47: 5 residues within 4Å: Chain G: Y.58 Ligands: UNL.46, UNL.48, UNL.53, UNL.54 Ligand excluded by PLIP UNL.48: 5 residues within 4Å: Chain E: H.216, I.218 Chain F: R.43 Ligands: UNL.47, UNL.54 Ligand excluded by PLIP UNL.49: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNL.53: 6 residues within 4Å: Chain E: P.169 Chain F: M.36, I.40 Ligands: UNL.46, UNL.47, UNL.54 Ligand excluded by PLIP UNL.54: 6 residues within 4Å: Chain E: I.218 Chain F: S.39, I.40 Ligands: UNL.47, UNL.48, UNL.53 Ligand excluded by PLIP UNL.55: 7 residues within 4Å: Chain F: V.53, F.56 Ligands: UNL.56, UNL.58, UNL.59, UNL.65, UNL.66 Ligand excluded by PLIP UNL.56: 6 residues within 4Å: Chain F: L.91 Ligands: UNL.55, UNL.58, UNL.59, UNL.64, UNL.65 Ligand excluded by PLIP UNL.57: 1 residues within 4Å: Chain F: S.96 Ligand excluded by PLIP UNL.58: 4 residues within 4Å: Ligands: UNL.55, UNL.56, UNL.59, UNL.66 Ligand excluded by PLIP UNL.59: 4 residues within 4Å: Ligands: UNL.55, UNL.56, UNL.58, UNL.65 Ligand excluded by PLIP UNL.60: 2 residues within 4Å: Chain F: W.32 Ligands: UNL.61 Ligand excluded by PLIP UNL.61: 3 residues within 4Å: Chain F: W.32, A.37 Ligands: UNL.60 Ligand excluded by PLIP UNL.62: 9 residues within 4Å: Chain F: S.50, S.54 Chain G: T.44, G.47, H.48, L.51, L.75, S.76, T.79 Ligand excluded by PLIP UNL.63: 1 residues within 4Å: Chain G: L.72 Ligand excluded by PLIP UNL.64: 6 residues within 4Å: Chain F: I.137, E.140 Chain G: V.97, A.98, W.101 Ligands: UNL.56 Ligand excluded by PLIP UNL.65: 5 residues within 4Å: Chain G: A.27, V.97 Ligands: UNL.55, UNL.56, UNL.59 Ligand excluded by PLIP UNL.66: 3 residues within 4Å: Chain F: F.56 Ligands: UNL.55, UNL.58 Ligand excluded by PLIP UNL.67: 2 residues within 4Å: Chain G: H.60 Ligands: UNL.68 Ligand excluded by PLIP UNL.68: 3 residues within 4Å: Chain G: Y.58 Ligands: UNL.67, UNL.69 Ligand excluded by PLIP UNL.69: 2 residues within 4Å: Ligands: UNL.68, UNL.70 Ligand excluded by PLIP UNL.70: 1 residues within 4Å: Ligands: UNL.69 Ligand excluded by PLIP UNL.71: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNL.72: 1 residues within 4Å: Chain G: Y.30 Ligand excluded by PLIP

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

FES.12: 9 residues within 4Å: Chain B: S.64, C.65, R.66, G.68, 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 FES.43: 11 residues within 4Å: Chain E: S.64, C.65, R.66, G.68, I.69, C.70, G.71, S.72, C.73, L.83, C.85 4 PLIP interactions: 4 interactions with chain E, Metal complexes: E:C.65, E:C.70, E:C.73, E:C.85

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

SF4.13: 12 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, K.227 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.158, B:C.161, B:C.164, B:C.225 SF4.44: 12 residues within 4Å: Chain E: C.158, I.159, L.160, C.161, A.162, C.163, C.164, A.182, M.185, C.225, P.226, K.227 4 PLIP interactions: 4 interactions with chain E, Metal complexes: E:C.158, E:C.161, E:C.164, E:C.225

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

F3S.14: 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 F3S.45: 11 residues within 4Å: Chain E: 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 E, Metal complexes: E:C.168, E:C.215, E:C.221

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.19: 8 residues within 4Å: Chain B: H.104, M.105, N.117, Y.171, G.175 Chain C: F.12, W.13, L.23 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.104, B:N.117 Water bridges: B:Y.106 GOL.50: 6 residues within 4Å: Chain E: H.104, M.105, Y.171 Chain F: F.12, W.13, L.23 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:H.104, E:N.117 Water bridges: E:Y.106

2 x BHG: hexyl beta-D-galactopyranoside(Non-covalent)

BHG.20: 7 residues within 4Å: Chain C: K.31, W.32, S.33, L.34, P.35, A.37, E.120 7 PLIP interactions: 6 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:A.37 Hydrogen bonds: C:K.31, C:K.31, C:W.32, C:L.34, C:E.120, B:R.223 BHG.51: 7 residues within 4Å: Chain E: R.223 Chain F: K.31, W.32, S.33, L.34, P.35, E.120 8 PLIP interactions: 6 interactions with chain F, 2 interactions with chain E Hydrogen bonds: F:K.31, F:W.32, F:L.34, F:E.120, E:R.223, E:R.223 Water bridges: F:K.31 Salt bridges: F:K.31

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

HEM.21: 17 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 20 PLIP interactions: 8 interactions with chain D, 10 interactions with chain C, 2 interactions with chain B, Hydrophobic interactions: D:L.20, D:L.43, C:L.49, C:L.49, C:H.105 Hydrogen bonds: D:G.50 Water bridges: D:R.14, C:H.105, C:H.105, C:H.105, B:H.216 Salt bridges: D:R.14, C:R.43, C:H.105, B:H.216 pi-Stacking: D:H.46, C:H.98 pi-Cation interactions: D:H.46 Metal complexes: D:H.46, C:H.98 HEM.52: 16 residues within 4Å: Chain E: H.216 Chain F: H.42, R.43, G.46, V.47, L.49, S.50, H.98, T.99, G.102, H.105 Chain G: R.14, L.20, L.43, H.46, G.50 18 PLIP interactions: 8 interactions with chain G, 8 interactions with chain F, 2 interactions with chain E, Hydrophobic interactions: G:L.20, G:L.43, F:L.49, F:L.49, F:H.105 Hydrogen bonds: G:G.50 Water bridges: G:R.14, G:R.14, F:H.105, F:H.105, E:H.216 Salt bridges: G:R.14, F:R.43, F:H.105, E:H.216 pi-Cation interactions: G:H.46 Metal complexes: G:H.46, F:H.98

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Huang, L.S. et al., Crystallographic studies of the binding of ligands to the dicarboxylate site of Complex II, and the identity of the ligand in the. Biochim.Biophys.Acta

Release Date

2006-06-20

Peptides

SUCCINATE DEHYDROGENASE FLAVOPROTEIN SUBUNIT: A
Succinate dehydrogenase Ip subunit: BE
SUCCINATE DEHYDROGENASE CYTOCHROME B, LARGE SUBUNIT: CF
Succinate dehydrogenase cytochrome B, small subunit: DG

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
O

E
B

C
P

F
C

D
Q

G
D

Membrane

We predict this structure to be a membrane protein.
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SUCCINATE DEHYDROGENASE FLAVOPROTEIN SUBUNIT

Succinate dehydrogenase Ip subunit

SUCCINATE DEHYDROGENASE CYTOCHROME B, LARGE SUBUNIT

Succinate dehydrogenase cytochrome B, small subunit

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