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

Remodelling of carboxin binding to the Q-site of avian respiratory complex II

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

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

UNL.1: 3 residues within 4Å: Chain A: Y.81, F.137, S.612 Ligand excluded by PLIP UNL.2: 2 residues within 4Å: Chain A: G.272, H.327 Ligand excluded by PLIP UNL.7: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNL.8: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNL.9: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNL.10: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNL.11: 3 residues within 4Å: Chain A: K.442, N.444, A.445 Ligand excluded by PLIP UNL.12: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNL.13: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNL.14: 1 residues within 4Å: Chain A: D.16 Ligand excluded by PLIP UNL.15: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNL.16: 3 residues within 4Å: Chain A: H.326, K.354, E.355 Ligand excluded by PLIP UNL.17: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNL.18: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNL.19: 1 residues within 4Å: Chain A: K.593 Ligand excluded by PLIP UNL.20: 1 residues within 4Å: Chain A: Y.500 Ligand excluded by PLIP UNL.21: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNL.22: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNL.23: 2 residues within 4Å: Chain A: H.326, H.327 Ligand excluded by PLIP UNL.24: 2 residues within 4Å: Chain A: K.495, Q.498 Ligand excluded by PLIP UNL.25: 3 residues within 4Å: Chain A: Y.563, L.567, P.615 Ligand excluded by PLIP UNL.27: 1 residues within 4Å: Chain B: D.46 Ligand excluded by PLIP UNL.28: 1 residues within 4Å: Chain B: P.209 Ligand excluded by PLIP UNL.29: 1 residues within 4Å: Chain B: D.22 Ligand excluded by PLIP UNL.30: 3 residues within 4Å: Chain B: T.8, R.10, N.38 Ligand excluded by PLIP UNL.31: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNL.35: 2 residues within 4Å: Chain B: A.78 Chain C: K.31 Ligand excluded by PLIP UNL.36: 1 residues within 4Å: Chain B: R.223 Ligand excluded by PLIP UNL.37: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNL.38: 1 residues within 4Å: Chain B: K.240 Ligand excluded by PLIP UNL.39: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNL.44: 2 residues within 4Å: Chain B: D.176 Chain C: W.13 Ligand excluded by PLIP UNL.45: 3 residues within 4Å: Chain C: Y.85, F.89, L.131 Ligand excluded by PLIP UNL.46: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNL.47: 1 residues within 4Å: Chain C: T.41 Ligand excluded by PLIP UNL.48: 1 residues within 4Å: Chain C: A.48 Ligand excluded by PLIP UNL.49: 3 residues within 4Å: Chain C: L.34, M.38 Ligands: UNL.50 Ligand excluded by PLIP UNL.50: 1 residues within 4Å: Ligands: UNL.49 Ligand excluded by PLIP UNL.51: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNL.52: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNL.53: 1 residues within 4Å: Chain C: Q.121 Ligand excluded by PLIP UNL.54: 1 residues within 4Å: Chain C: S.122 Ligand excluded by PLIP UNL.55: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNL.56: 2 residues within 4Å: Chain C: E.120 Ligands: BHG.41 Ligand excluded by PLIP UNL.57: 1 residues within 4Å: Chain C: L.61 Ligand excluded by PLIP UNL.58: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNL.61: 1 residues within 4Å: Chain D: Y.73 Ligand excluded by PLIP UNL.62: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNL.63: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNL.64: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNL.65: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNL.66: 1 residues within 4Å: Chain D: T.70 Ligand excluded by PLIP UNL.67: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNL.68: 1 residues within 4Å: Chain D: Y.58 Ligand excluded by PLIP UNL.69: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP

2 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 K.26: 4 residues within 4Å: Chain B: M.191, D.193, D.196, T.199 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:M.191, B:D.193, B:D.196, B:T.199, H2O.31

1 x AZI: AZIDE ION(Non-covalent)

AZI.4: 3 residues within 4Å: Chain A: Y.172, F.173, V.174 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.172, A:V.174 Water bridges: A:Y.176

1 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Covalent)

FAD.5: 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: OAA.6 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:T.57, A:T.57, A:Q.61, 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:H.56, A:H.56, A:G.215, A:D.232, A:E.397, A:E.397, A:A.398 pi-Cation interactions: A:H.364

1 x OAA: OXALOACETATE ION(Non-covalent)

OAA.6: 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.5 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:F.130 Hydrogen bonds: A:G.62, 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 FES: FE2/S2 (INORGANIC) CLUSTER(Non-covalent)

FES.32: 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)

SF4.33: 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

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

F3S.34: 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

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.40: 7 residues within 4Å: Chain B: H.104, M.105, Y.171, G.175 Chain C: F.12, W.13, L.23 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:H.104 Water bridges: B:Y.106, B:N.117, B:N.117 GOL.59: 5 residues within 4Å: Chain C: F.56 Chain D: L.83, I.93, V.97 Ligands: PEE.60 No protein-ligand interaction detected (PLIP)

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

BHG.41: 8 residues within 4Å: Chain B: R.223 Chain C: K.31, W.32, S.33, L.34, P.35, E.120 Ligands: UNL.56 8 PLIP interactions: 2 interactions with chain B, 6 interactions with chain C Hydrogen bonds: B:R.223, B:R.223, C:K.31, C:K.31, C:L.34, C:E.120 Water bridges: C:K.31, C:W.32

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

HEM.42: 18 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 Ligands: CBE.43 19 PLIP interactions: 8 interactions with chain C, 10 interactions with chain D, 1 interactions with chain B, Hydrophobic interactions: C:L.49, C:L.49, C:H.105, D:L.20, D:L.43 Water bridges: C:H.105, D:R.14, D:R.14, D:R.14, D:R.14 Salt bridges: C:R.43, C:H.105, D:R.14 pi-Stacking: C:H.98, D:H.46, D:H.46 Metal complexes: C:H.98, D:H.46 Hydrogen bonds: B:H.216

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

CBE.43: 14 residues within 4Å: Chain B: P.169, S.170, W.173, H.216, I.218 Chain C: I.27, W.32, M.36, S.39, I.40, R.43 Chain D: D.57, Y.58 Ligands: HEM.42 7 PLIP interactions: 5 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:I.27, C:I.27, C:W.32, C:I.40, B:P.169, B:W.173 Water bridges: C:S.39

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

PEE.60: 6 residues within 4Å: Chain C: I.140 Chain D: A.27, Y.28, C.94, W.101 Ligands: GOL.59 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:A.27, D:W.101, D:W.101, D:W.101, C:I.140

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ruprecht, J. et al., Remodelling of Carboxin Binding to the Q-Site of Avian Respiratory Complex II. To be Published

Release Date

2010-08-25

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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