SMTL ID : 1zoy.1

Crystal Structure of Mitochondrial Respiratory Complex II from porcine heart at 2.4 Angstroms

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 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.25, G.26, A.27, G.28, G.29, A.30, V.48, T.49, K.50, L.51, S.56, H.57, T.58, A.60, A.61, Q.62, G.63, G.64, Y.177, F.178, A.179, A.213, T.214, G.215, T.225, S.226, D.233, L.264, H.365, Y.366, G.397, E.398, R.409, A.412, N.413, S.414, L.415, L.418 33 PLIP interactions: 33 interactions with chain A Hydrophobic interactions: A:A.60, A:L.264 Hydrogen bonds: A:A.27, A:A.27, A:A.30, A:K.50, A:K.50, A:L.51, A:H.57, A:T.58, A:Q.62, A:G.63, A:G.64, A:G.64, A:A.179, A:A.179, A:G.215, A:E.398, A:E.398, A:R.409, A:R.409, A:A.412, A:S.414, A:S.414, A:L.415 Water bridges: A:G.28, A:G.216, A:R.298, A:R.298, A:E.398, A:A.399, A:R.409 pi-Cation interactions: A:H.365

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

FES.2: 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)

SF4.3: 10 residues within 4Å: Chain B: C.158, I.159, L.160, C.161, A.162, C.163, C.164, C.225, P.226, P.231 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.4: 11 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 3 PLIP interactions: 3 interactions with chain B, Metal complexes: B:C.168, B:C.215, B:C.221

1 x UQ1: UBIQUINONE-1(Non-covalent)

UQ1.5: 10 residues within 4Å: Chain B: P.169, W.173, I.218 Chain C: I.27, W.32, M.36, S.39, I.40, R.43 Chain D: Y.58 8 PLIP interactions: 7 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:I.27, C:I.27, C:W.32, C:W.32, C:I.40, C:I.40, B:W.173 Hydrogen bonds: C:R.43

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

HEM.6: 23 residues within 4Å: Chain B: H.216 Chain C: H.42, R.43, G.46, I.47, L.49, S.50, V.53, L.95, H.98, T.99, G.102, H.105 Chain D: R.14, S.17, L.20, L.24, L.43, H.46, G.50, I.51, Q.53, V.54 24 PLIP interactions: 11 interactions with chain C, 10 interactions with chain D, 3 interactions with chain B, Hydrophobic interactions: C:L.49, C:V.53, C:L.95, C:T.99, C:H.105, D:L.20, D:L.24, D:L.43, D:I.51 Salt bridges: C:R.43, C:H.105, D:R.14, B:H.216, B:H.216 pi-Stacking: C:H.42, C:H.42, C:H.98, D:H.46, D:H.46, D:H.46 Metal complexes: C:H.98, D:H.46 pi-Cation interactions: D:H.46 Water bridges: B:H.216

2 x EPH: L-ALPHA-PHOSPHATIDYL-BETA-OLEOYL-GAMMA-PALMITOYL-PHOSPHATIDYLETHANOLAMINE(Non-covalent)

EPH.7: 10 residues within 4Å: Chain C: V.53, F.56 Chain D: L.24, A.27, Y.28, P.31, L.39, V.97, A.98, W.101 10 PLIP interactions: 8 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:L.24, D:Y.28, D:L.39, D:W.101, D:W.101, D:W.101, C:V.53, C:F.56 Hydrogen bonds: D:Y.28 Water bridges: D:K.102 EPH.8: 4 residues within 4Å: Chain D: H.48, K.66, A.70, L.73 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:A.70 Hydrogen bonds: D:H.48 Salt bridges: D:K.66

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sun, F. et al., Crystal Structure of Mitochondrial Respiratory Membrane Protein Complex II. Cell(Cambridge,Mass.) (2005)

Release Date

2005-07-12

Peptides

FAD-binding protein: A
Iron-sulfur protein: B
Large cytochrome binding protein: C
Small cytochrome binding protein: 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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FAD-binding protein

Iron-sulfur protein

Large cytochrome binding protein

Small cytochrome binding protein

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