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

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 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 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:N.366, A:G.368, A:E.397, A:A.399 K.25: 4 residues within 4Å: Chain B: M.191, D.193, D.196, T.199 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:M.191, B:D.193, B:D.196, B:T.199

1 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Covalent)

FAD.2: 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.3 36 PLIP interactions: 36 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:E.397, A:E.397, A:A.398 pi-Cation interactions: A:H.364

1 x OAA: OXALOACETATE ION(Non-covalent)

OAA.3: 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.2 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:F.130 Hydrogen bonds: A:G.62, A:T.265, 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

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

UNL.4: 4 residues within 4Å: Chain A: Q.11, Y.12, R.457, I.513 Ligand excluded by PLIP UNL.5: 3 residues within 4Å: Chain A: A.240, L.242 Ligands: UNL.11 Ligand excluded by PLIP UNL.6: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNL.7: 1 residues within 4Å: Chain A: N.75 Ligand excluded by PLIP UNL.8: 1 residues within 4Å: Chain A: E.608 Ligand excluded by PLIP UNL.9: 1 residues within 4Å: Chain A: Q.332 Ligand excluded by PLIP UNL.10: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNL.11: 2 residues within 4Å: Chain A: T.380 Ligands: UNL.5 Ligand excluded by PLIP UNL.12: 1 residues within 4Å: Chain A: Y.258 Ligand excluded by PLIP UNL.13: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNL.14: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNL.15: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNL.16: 1 residues within 4Å: Chain A: E.447 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: Q.324 Ligand excluded by PLIP UNL.20: 2 residues within 4Å: Chain A: E.491, E.494 Ligand excluded by PLIP UNL.21: 2 residues within 4Å: Chain A: D.16, E.18 Ligand excluded by PLIP UNL.22: 3 residues within 4Å: Chain A: K.474, Q.477, S.478 Ligand excluded by PLIP UNL.23: 1 residues within 4Å: Chain A: K.474 Ligand excluded by PLIP UNL.24: 1 residues within 4Å: Chain A: P.329 Ligand excluded by PLIP UNL.26: 1 residues within 4Å: Chain B: P.28 Ligand excluded by PLIP UNL.27: 1 residues within 4Å: Chain B: A.243 Ligand excluded by PLIP UNL.31: 2 residues within 4Å: Chain B: D.176 Chain C: W.13 Ligand excluded by PLIP UNL.32: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNL.33: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNL.34: 2 residues within 4Å: Chain B: K.177, F.210 Ligand excluded by PLIP UNL.40: 3 residues within 4Å: Chain C: G.52 Ligands: GOL.39, PEE.47 Ligand excluded by PLIP UNL.41: 2 residues within 4Å: Chain C: A.60 Chain D: F.86 Ligand excluded by PLIP UNL.42: 1 residues within 4Å: Chain C: Q.118 Ligand excluded by PLIP UNL.43: 1 residues within 4Å: Chain C: G.113 Ligand excluded by PLIP UNL.44: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNL.45: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNL.46: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNL.48: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNL.49: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNL.50: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNL.51: 2 residues within 4Å: Chain D: G.22, A.26 Ligand excluded by PLIP UNL.52: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP UNL.53: 1 residues within 4Å: Chain D: Y.73 Ligand excluded by PLIP

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

FES.28: 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)

SF4.29: 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.30: 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.35: 9 residues within 4Å: Chain B: H.104, M.105, Y.106, N.117, 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, B:N.117 Water bridges: B:Y.171, B:G.175 GOL.39: 4 residues within 4Å: Chain C: L.49, L.91 Ligands: UNL.40, PEE.47 No protein-ligand interaction detected (PLIP)

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

HEM.36: 17 residues within 4Å: Chain B: H.216 Chain C: H.42, R.43, G.46, 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 18 PLIP interactions: 9 interactions with chain D, 8 interactions with chain C, 1 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, B:H.216 Water bridges: D:R.14, D:R.14, C:H.105 Salt bridges: D:R.14, C:R.43, C:H.105 pi-Stacking: D:H.46, D:H.46, C:H.98 Metal complexes: D:H.46, C:H.98

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

CBE.37: 13 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 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 BHG: hexyl beta-D-galactopyranoside(Non-covalent)

BHG.38: 8 residues within 4Å: Chain B: R.223 Chain C: K.31, W.32, S.33, L.34, P.35, A.37, E.120 7 PLIP interactions: 5 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:A.37 Hydrogen bonds: C:L.34, C:E.120, B:R.223, B:R.223 Water bridges: C:K.31, C:W.32

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

PEE.47: 10 residues within 4Å: Chain C: I.140, S.141 Chain D: A.27, Y.28, C.94, V.97, A.98, W.101 Ligands: GOL.39, UNL.40 4 PLIP interactions: 1 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: C:I.140, D:A.27, D:W.101, D:W.101

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
N

B
O

C
P

D
Q

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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