SMTL ID : 2h89.1

Avian Respiratory Complex II with Malonate Bound

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

2 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 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:N.366, A:M.367, A:G.368, A:E.397, A:A.399 K.19: 4 residues within 4Å: Chain B: M.191, D.193, D.196, T.199 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:M.191, H2O.13, H2O.14, H2O.18

1 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Covalent)

FAD.2: 38 residues within 4Å: Chain A: 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, S.225, 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: MLI.3 30 PLIP interactions: 30 interactions with chain A Hydrophobic interactions: A:L.263, A:L.263 Hydrogen bonds: A:A.26, A:A.26, A:G.28, A:A.29, A:K.49, A:K.49, A:L.50, A:T.57, A:T.57, A:Q.61, A:G.63, 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:H.56, A:H.56, A:Y.365, A:A.398 pi-Cation interactions: A:H.364

1 x MLI: MALONATE ION(Non-functional Binders)

MLI.3: 12 residues within 4Å: Chain A: G.62, F.130, H.253, L.263, T.265, E.266, R.297, H.364, R.408, G.410, A.411 Ligands: FAD.2 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:L.263 Hydrogen bonds: A:G.62, A:E.266, A:A.411 Salt bridges: A:H.253, A:R.297, A:R.297, A:H.364, A:R.408

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

UNL.4: 3 residues within 4Å: Chain A: H.326, H.327 Ligands: UNL.16 Ligand excluded by PLIP UNL.5: 2 residues within 4Å: Chain A: Q.490, E.540 Ligand excluded by PLIP UNL.6: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNL.7: 3 residues within 4Å: Chain A: I.602, D.603, R.604 Ligand excluded by PLIP UNL.8: 2 residues within 4Å: Chain A: A.429, E.430 Ligand excluded by PLIP UNL.9: 3 residues within 4Å: Chain A: P.330, Q.331, A.334 Ligand excluded by PLIP UNL.10: 2 residues within 4Å: Chain A: D.73 Ligands: UNL.11 Ligand excluded by PLIP UNL.11: 2 residues within 4Å: Chain A: W.78 Ligands: UNL.10 Ligand excluded by PLIP UNL.12: 2 residues within 4Å: Chain A: S.620, Y.621 Ligand excluded by PLIP UNL.13: 3 residues within 4Å: Chain A: T.475, K.495, I.499 Ligand excluded by PLIP UNL.14: 3 residues within 4Å: Chain A: R.309, E.310, G.311 Ligand excluded by PLIP UNL.15: 1 residues within 4Å: Chain A: E.608 Ligand excluded by PLIP UNL.16: 2 residues within 4Å: Chain A: P.329 Ligands: UNL.4 Ligand excluded by PLIP UNL.17: 4 residues within 4Å: Chain A: F.80, F.137, S.612, V.614 Ligand excluded by PLIP UNL.18: 1 residues within 4Å: Chain A: G.241 Ligand excluded by PLIP UNL.23: 3 residues within 4Å: Chain B: I.11, K.13, L.93 Ligand excluded by PLIP UNL.24: 5 residues within 4Å: Chain B: W.173 Chain C: R.43 Chain D: Y.58 Ligands: UNL.25, UNL.37 Ligand excluded by PLIP UNL.25: 5 residues within 4Å: Chain B: P.169, I.218 Ligands: UNL.24, UNL.36, UNL.37 Ligand excluded by PLIP UNL.26: 1 residues within 4Å: Chain B: D.22 Ligand excluded by PLIP UNL.27: 1 residues within 4Å: Chain B: T.199 Ligand excluded by PLIP UNL.28: 2 residues within 4Å: Chain B: H.104, W.173 Ligand excluded by PLIP UNL.29: 2 residues within 4Å: Chain B: K.177, F.210 Ligand excluded by PLIP UNL.30: 1 residues within 4Å: Chain A: E.121 Ligand excluded by PLIP UNL.31: 4 residues within 4Å: Chain B: Q.207, D.208, P.209 Chain D: A.6 Ligand excluded by PLIP UNL.32: 1 residues within 4Å: Chain B: K.139 Ligand excluded by PLIP UNL.36: 3 residues within 4Å: Chain C: M.36, I.40 Ligands: UNL.25 Ligand excluded by PLIP UNL.37: 5 residues within 4Å: Chain B: I.218 Chain C: S.39 Ligands: UNL.24, UNL.25, UNL.38 Ligand excluded by PLIP UNL.38: 5 residues within 4Å: Chain B: H.216 Chain C: S.39, R.43 Ligands: HEM.34, UNL.37 Ligand excluded by PLIP UNL.39: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNL.40: 2 residues within 4Å: Chain C: F.56, F.67 Ligand excluded by PLIP UNL.41: 2 residues within 4Å: Chain A: Y.162 Chain C: E.8 Ligand excluded by PLIP UNL.42: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNL.43: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNL.44: 2 residues within 4Å: Chain C: L.58, A.59 Ligand excluded by PLIP UNL.46: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNL.47: 1 residues within 4Å: Chain D: Y.28 Ligand excluded by PLIP UNL.48: 1 residues within 4Å: Chain D: L.19 Ligand excluded by PLIP UNL.49: 1 residues within 4Å: Chain D: H.9 Ligand excluded by PLIP UNL.50: 1 residues within 4Å: Chain D: A.41 Ligand excluded by PLIP UNL.51: 2 residues within 4Å: Chain D: Y.30, P.31 Ligand excluded by PLIP

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

FES.20: 10 residues within 4Å: Chain B: 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)

SF4.21: 11 residues within 4Å: Chain B: C.158, I.159, L.160, C.161, A.162, C.163, C.164, 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

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

F3S.22: 12 residues within 4Å: Chain B: C.168, S.170, 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 BHG: hexyl beta-D-galactopyranoside(Non-covalent)

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

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

HEM.34: 19 residues within 4Å: Chain B: H.216 Chain C: H.42, R.43, G.46, V.47, L.49, S.50, L.95, H.98, T.99, G.102, H.105 Chain D: R.14, L.20, L.24, H.46, G.50, L.51 Ligands: UNL.38 20 PLIP interactions: 7 interactions with chain D, 12 interactions with chain C, 1 interactions with chain B, Hydrophobic interactions: D:L.20, D:L.24, D:L.51, C:L.49, C:L.49, C:L.95, C:T.99, C:H.105 Hydrogen bonds: D:R.14, D:G.50 Water bridges: D:R.14, C:H.42, C:H.105, C:H.105, C:H.105 Metal complexes: D:H.46, C:H.98 Salt bridges: C:R.43, C:H.105, B:H.216

2 x PEE: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine(Non-covalent)

PEE.35: 3 residues within 4Å: Chain C: S.96, W.100 Chain D: L.21 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:L.21, D:L.21, C:W.100, C:W.100 PEE.45: 9 residues within 4Å: Chain C: L.91, I.137, E.140 Chain D: A.27, Y.28, P.31, C.94, V.97, W.101 11 PLIP interactions: 9 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:A.27, D:Y.28, D:P.31, D:V.97, D:V.97, D:W.101, D:W.101, D:W.101, D:W.101, C:L.91, C:I.137

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: B
SUCCINATE DEHYDROGENASE CYTOCHROME B, LARGE SUBUNIT: C
SUCCINATE DEHYDROGENASE CYTOCHROME B, SMALL SUBUNIT: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
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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