SMTL ID : 1sqp.1

Crystal Structure Analysis of Bovine Bc1 with Myxothiazol

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

hetero-oligomer

Ligands

6 x PEE: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE(Non-covalent)

PEE.1: 21 residues within 4Å: Chain C: L.43, L.46, M.82, I.236, M.240 Chain J: D.36 Chain E: Y.49, A.50, N.53, V.54, Q.57, F.58, V.59 Chain D: H.200, M.204, K.207, M.208, M.211, M.212 Ligands: PEE.5, PLX.7 17 PLIP interactions: 4 interactions with chain C, 2 interactions with chain J, 8 interactions with chain E, 3 interactions with chain D Hydrophobic interactions: C:L.43, C:L.46, C:I.236, C:I.236, E:A.50, E:V.54, E:V.54, E:F.58, E:F.58, E:F.58, E:V.59, D:M.211 Hydrogen bonds: J:D.36, J:D.36, E:Q.57 Salt bridges: D:H.200, D:K.207 PEE.5: 8 residues within 4Å: Chain A: S.473, F.476, L.478 Chain C: V.14, H.221 Ligands: PEE.1, CDL.2, PLX.7 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain C Hydrogen bonds: A:S.473, A:S.473 Hydrophobic interactions: C:V.14 Salt bridges: C:H.221, C:H.221 PEE.6: 19 residues within 4Å: Chain C: W.30, Y.95, M.96, G.99, R.100, Y.103, Y.104, F.276, I.298, M.316, F.325, W.326, V.329, L.332, T.336, Y.358 Ligands: CDL.4 Chain G: V.48 Chain F: Q.72 17 PLIP interactions: 16 interactions with chain C, 1 interactions with chain F Hydrophobic interactions: C:W.30, C:W.30, C:W.30, C:W.30, C:Y.95, C:F.276, C:I.298, C:F.325, C:F.325, C:W.326, C:W.326, C:V.329 Hydrogen bonds: C:W.30, C:Y.103, C:Y.103, C:Y.104, F:Q.72 PEE.13: 21 residues within 4Å: Chain P: Y.49, A.50, N.53, V.54, Q.57, F.58, V.59 Chain U: D.36 Ligands: PEE.17, PLX.19 Chain O: H.200, M.204, K.207, M.208, M.211, M.212 Chain N: L.43, L.46, M.82, I.236, M.240 17 PLIP interactions: 8 interactions with chain P, 2 interactions with chain U, 3 interactions with chain O, 4 interactions with chain N Hydrophobic interactions: P:A.50, P:V.54, P:V.54, P:F.58, P:F.58, P:F.58, P:V.59, O:M.211, N:L.43, N:L.46, N:I.236, N:I.236 Hydrogen bonds: P:Q.57, U:D.36, U:D.36 Salt bridges: O:H.200, O:K.207 PEE.17: 8 residues within 4Å: Chain L: S.473, F.476, L.478 Ligands: PEE.13, CDL.14, PLX.19 Chain N: V.14, H.221 5 PLIP interactions: 2 interactions with chain L, 3 interactions with chain N Hydrogen bonds: L:S.473, L:S.473 Hydrophobic interactions: N:V.14 Salt bridges: N:H.221, N:H.221 PEE.18: 19 residues within 4Å: Chain Q: Q.72 Chain R: V.48 Ligands: CDL.16 Chain N: W.30, Y.95, M.96, G.99, R.100, Y.103, Y.104, F.276, I.298, M.316, F.325, W.326, V.329, L.332, T.336, Y.358 17 PLIP interactions: 1 interactions with chain Q, 16 interactions with chain N Hydrogen bonds: Q:Q.72, N:W.30, N:Y.103, N:Y.103, N:Y.104 Hydrophobic interactions: N:W.30, N:W.30, N:W.30, N:W.30, N:Y.95, N:F.276, N:I.298, N:F.325, N:F.325, N:W.326, N:W.326, N:V.329

6 x CDL: CARDIOLIPIN(Non-covalent)

CDL.2: 11 residues within 4Å: Chain A: F.370, W.477, L.478, R.479 Chain C: R.5, I.19, H.221, T.225, I.229 Chain K: W.24 Ligands: PEE.5 10 PLIP interactions: 4 interactions with chain A, 5 interactions with chain C, 1 interactions with chain K Hydrophobic interactions: A:L.478, C:I.19, C:T.225, C:I.229, K:W.24 Hydrogen bonds: A:L.478, A:R.479 Salt bridges: A:R.479, C:R.5, C:H.221 CDL.3: 20 residues within 4Å: Ligands: CDL.4 Chain C: S.29, N.32, F.33, L.36, K.227, L.230, G.231, L.234 Chain D: P.217, Y.220, K.223, R.224, K.231 Chain G: Y.29, G.33, N.36, V.37, R.40 Chain F: R.71 18 PLIP interactions: 3 interactions with chain C, 8 interactions with chain D, 7 interactions with chain G Hydrophobic interactions: C:F.33, C:L.36, D:P.217, D:Y.220 Hydrogen bonds: D:Y.220, D:R.224, G:Y.29, G:Y.29, G:Y.29, G:N.36, G:R.40, G:R.40 Salt bridges: C:K.227, D:K.223, D:K.223, D:R.224, D:K.231, G:R.40 CDL.4: 10 residues within 4Å: Chain C: S.28, S.29, W.30, F.33 Ligands: CDL.3, PEE.6 Chain G: R.40, T.41, C.44 Chain F: Q.72 10 PLIP interactions: 4 interactions with chain C, 4 interactions with chain G, 2 interactions with chain F Hydrogen bonds: C:S.28, C:S.29, C:S.29, C:W.30, F:Q.72, F:Q.72 Hydrophobic interactions: G:T.41 Salt bridges: G:R.40, G:R.40, G:R.40 CDL.14: 11 residues within 4Å: Chain V: W.24 Chain L: F.370, W.477, L.478, R.479 Ligands: PEE.17 Chain N: R.5, I.19, H.221, T.225, I.229 10 PLIP interactions: 5 interactions with chain N, 4 interactions with chain L, 1 interactions with chain V Hydrophobic interactions: V:W.24, L:L.478, N:I.19, N:T.225, N:I.229 Hydrogen bonds: L:L.478, L:R.479 Salt bridges: L:R.479, N:R.5, N:H.221 CDL.15: 20 residues within 4Å: Chain Q: R.71 Chain R: Y.29, G.33, N.36, V.37, R.40 Ligands: CDL.16 Chain O: P.217, Y.220, K.223, R.224, K.231 Chain N: S.29, N.32, F.33, L.36, K.227, L.230, G.231, L.234 18 PLIP interactions: 7 interactions with chain R, 8 interactions with chain O, 3 interactions with chain N Hydrogen bonds: R:Y.29, R:Y.29, R:Y.29, R:N.36, R:R.40, R:R.40, O:Y.220, O:R.224 Hydrophobic interactions: O:P.217, O:Y.220, N:F.33, N:L.36 Salt bridges: R:R.40, O:K.223, O:K.223, O:R.224, O:K.231, N:K.227 CDL.16: 10 residues within 4Å: Chain Q: Q.72 Chain R: R.40, T.41, C.44 Ligands: CDL.15, PEE.18 Chain N: S.28, S.29, W.30, F.33 10 PLIP interactions: 2 interactions with chain Q, 4 interactions with chain R, 4 interactions with chain N Hydrogen bonds: Q:Q.72, Q:Q.72, N:S.28, N:S.29, N:S.29, N:W.30 Hydrophobic interactions: R:T.41 Salt bridges: R:R.40, R:R.40, R:R.40

2 x PLX: (9R,11S)-9-({[(1S)-1-HYDROXYHEXADECYL]OXY}METHYL)-2,2-DIMETHYL-5,7,10-TRIOXA-2LAMBDA~5~-AZA-6LAMBDA~5~-PHOSPHAOCTACOSANE-6,6,11-TRIOL(Non-covalent)

PLX.7: 17 residues within 4Å: Chain A: D.451, F.476, L.478 Chain C: A.232, L.233 Chain E: Y.37, T.40 Chain D: M.222 Chain J: F.14, R.15, T.17, F.20, A.21, I.24, V.25 Ligands: PEE.1, PEE.5 10 PLIP interactions: 2 interactions with chain A, 2 interactions with chain C, 4 interactions with chain J, 2 interactions with chain E Hydrophobic interactions: C:A.232, C:L.233, J:A.21, J:I.24, J:V.25 Hydrogen bonds: E:T.40 Salt bridges: A:D.451 pi-Cation interactions: A:F.476, J:F.20, E:Y.37 PLX.19: 17 residues within 4Å: Chain L: D.451, F.476, L.478 Chain O: M.222 Chain N: A.232, L.233 Chain P: Y.37, T.40 Chain U: F.14, R.15, T.17, F.20, A.21, I.24, V.25 Ligands: PEE.13, PEE.17 10 PLIP interactions: 2 interactions with chain P, 4 interactions with chain U, 2 interactions with chain L, 2 interactions with chain N Hydrogen bonds: P:T.40 Hydrophobic interactions: U:A.21, U:I.24, U:V.25, N:A.232, N:L.233 Salt bridges: L:D.451 pi-Cation interactions: P:Y.37, U:F.20, L:F.476

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

HEM.8: 21 residues within 4Å: Chain C: W.31, G.34, S.35, L.37, G.38, L.94, H.97, V.98, R.100, S.106, T.112, W.113, G.116, V.117, L.119, L.120, H.196, L.197, L.200, S.205, N.206 22 PLIP interactions: 22 interactions with chain C, Hydrophobic interactions: C:L.37, C:L.37, C:L.37, C:W.113, C:W.113, C:W.113, C:V.117, C:L.119, C:L.120, C:L.197, C:L.200, C:L.200 Hydrogen bonds: C:W.31, C:G.34, C:S.106, C:S.205, C:N.206 Salt bridges: C:H.97, C:R.100, C:R.100 Metal complexes: C:H.97, C:H.196 HEM.9: 22 residues within 4Å: Chain C: Q.44, I.45, G.48, L.49, L.51, Y.55, R.80, H.83, A.84, A.87, T.126, A.127, G.130, Y.131, L.133, P.134, F.179, H.182, F.183, P.186, I.189, Y.273 18 PLIP interactions: 18 interactions with chain C, Hydrophobic interactions: C:Q.44, C:I.45, C:L.51, C:Y.55, C:A.84, C:T.126, C:L.133, C:L.133, C:F.179, C:F.183, C:F.183, C:P.186, C:P.186, C:I.189 Salt bridges: C:R.80, C:R.80 Metal complexes: C:H.83, C:H.182 HEM.10: 23 residues within 4Å: Chain D: V.32, V.36, C.37, C.40, H.41, N.105, A.108, L.109, P.110, P.111, L.113, I.116, R.120, Y.126, V.127, L.130, L.131, F.153, I.158, G.159, M.160, P.163, V.186 13 PLIP interactions: 13 interactions with chain D, Hydrophobic interactions: D:V.32, D:V.36, D:P.110, D:L.113, D:I.116, D:V.127, D:L.130, D:L.131, D:M.160, D:P.163, D:V.186 Salt bridges: D:R.120 Metal complexes: D:H.41 HEM.20: 21 residues within 4Å: Chain N: W.31, G.34, S.35, L.37, G.38, L.94, H.97, V.98, R.100, S.106, T.112, W.113, G.116, V.117, L.119, L.120, H.196, L.197, L.200, S.205, N.206 22 PLIP interactions: 22 interactions with chain N Hydrophobic interactions: N:L.37, N:L.37, N:L.37, N:W.113, N:W.113, N:W.113, N:V.117, N:L.119, N:L.120, N:L.197, N:L.200, N:L.200 Hydrogen bonds: N:W.31, N:G.34, N:S.106, N:S.205, N:N.206 Salt bridges: N:H.97, N:R.100, N:R.100 Metal complexes: N:H.97, N:H.196 HEM.21: 22 residues within 4Å: Chain N: Q.44, I.45, G.48, L.49, L.51, Y.55, R.80, H.83, A.84, A.87, T.126, A.127, G.130, Y.131, L.133, P.134, F.179, H.182, F.183, P.186, I.189, Y.273 18 PLIP interactions: 18 interactions with chain N Hydrophobic interactions: N:Q.44, N:I.45, N:L.51, N:Y.55, N:A.84, N:T.126, N:L.133, N:L.133, N:F.179, N:F.183, N:F.183, N:P.186, N:P.186, N:I.189 Salt bridges: N:R.80, N:R.80 Metal complexes: N:H.83, N:H.182 HEM.22: 23 residues within 4Å: Chain O: V.32, V.36, C.37, C.40, H.41, N.105, A.108, L.109, P.110, P.111, L.113, I.116, R.120, Y.126, V.127, L.130, L.131, F.153, I.158, G.159, M.160, P.163, V.186 13 PLIP interactions: 13 interactions with chain O, Hydrophobic interactions: O:V.32, O:V.36, O:P.110, O:L.113, O:I.116, O:V.127, O:L.130, O:L.131, O:M.160, O:P.163, O:V.186 Salt bridges: O:R.120 Metal complexes: O:H.41

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

FES.11: 10 residues within 4Å: Chain E: C.139, H.141, L.142, G.143, C.144, C.158, C.160, H.161, G.162, S.163 2 PLIP interactions: 2 interactions with chain E, Metal complexes: E:C.158, E:H.161 FES.23: 10 residues within 4Å: Chain P: C.139, H.141, L.142, G.143, C.144, C.158, C.160, H.161, G.162, S.163 2 PLIP interactions: 2 interactions with chain P, Metal complexes: P:C.158, P:H.161

2 x MYX: (2Z,6E)-7-{2'-[(2E,4E)-1,6-DIMETHYLHEPTA-2,4-DIENYL]-2,4'-BI-1,3-THIAZOL-4-YL}-3,5-DIMETHOXY-4-METHYLHEPTA-2,6-DIENAMIDE(Non-covalent)

MYX.12: 19 residues within 4Å: Chain C: L.121, M.124, A.125, A.127, F.128, Y.131, V.132, M.138, G.142, A.143, V.145, I.146, K.269, P.270, E.271, Y.273, F.274, Y.278, L.294 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:L.121, C:L.121, C:A.125, C:Y.131, C:I.146, C:I.146, C:P.270, C:F.274 Hydrogen bonds: C:A.127, C:E.271, C:Y.273 pi-Stacking: C:F.274 MYX.24: 19 residues within 4Å: Chain N: L.121, M.124, A.125, A.127, F.128, Y.131, V.132, M.138, G.142, A.143, V.145, I.146, K.269, P.270, E.271, Y.273, F.274, Y.278, L.294 12 PLIP interactions: 12 interactions with chain N Hydrophobic interactions: N:L.121, N:L.121, N:A.125, N:Y.131, N:I.146, N:I.146, N:P.270, N:F.274 Hydrogen bonds: N:A.127, N:E.271, N:Y.273 pi-Stacking: N:F.274

Links

RCSB   PDBe   PDBj   PDBsum   CATH   PLIP

Citation

Esser, L. et al., Crystallographic studies of quinol oxidation site inhibitors: a modified classification of inhibitors for the cytochrome bc(1) complex. J.Mol.Biol. (2004)

Release Date

2005-11-01

Peptides

Ubiquinol-cytochrome-c reductase complex core protein I, mitochondrial precursor: AL
Ubiquinol-cytochrome-c reductase complex core protein 2, mitochondrial precursor: BM
Cytochrome b: CN
Cytochrome c1, heme protein, mitochondrial: DO
Ubiquinol-cytochrome c reductase iron-sulfur subunit, mitochondrial precursor (EC 1.10.2.2) (Rieske iron-sulfur protein) (RISP) [Contains: Ubiquinol-cytochrome c reductase 8 kDa protein (Complex III subunit IX)]: EP
sub6: FQ
Ubiquinol-cytochrome c reductase complex ubiquinone-binding protein QP-C: GR
Ubiquinol-cytochrome c reductase complex 11 kDa protein: HS
Ubiquinol-cytochrome c reductase iron-sulfur subunit, mitochondrial precursor (EC 1.10.2.2) (Rieske iron-sulfur protein) (RISP) [Contains: Ubiquinol-cytochrome c reductase 8 kDa protein (Complex III subunit IX)]: IT
Ubiquinol-cytochrome c reductase complex 7.2 kDa protein: JU
Ubiquinol-cytochrome c reductase complex 6.4 kDa protein: KV

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

L
A

B
B

M
B

C
C

N
C

D
D

O
D

E
E

P
E

F
F

Q
F

G
G

R
G

H
H

S
H

I
I

T
I

J
J

U
J

K
K

V
K

Ubiquinol-cytochrome-c reductase complex core protein I, mitochondrial precursor

Ubiquinol-cytochrome-c reductase complex core protein 2, mitochondrial precursor

Cytochrome b

Cytochrome c1, heme protein, mitochondrial

Ubiquinol-cytochrome c reductase iron-sulfur subunit, mitochondrial precursor (EC 1.10.2.2) (Rieske iron-sulfur protein) (RISP) [Contains: Ubiquinol-cytochrome c reductase 8 kDa protein (Complex III subunit IX)]

sub6

Ubiquinol-cytochrome c reductase complex ubiquinone-binding protein QP-C

Ubiquinol-cytochrome c reductase complex 11 kDa protein

Ubiquinol-cytochrome c reductase iron-sulfur subunit, mitochondrial precursor (EC 1.10.2.2) (Rieske iron-sulfur protein) (RISP) [Contains: Ubiquinol-cytochrome c reductase 8 kDa protein (Complex III subunit IX)]

Ubiquinol-cytochrome c reductase complex 7.2 kDa protein

Ubiquinol-cytochrome c reductase complex 6.4 kDa protein

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