- 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)
- 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:1 interactions with chain K, 5 interactions with chain C, 4 interactions with chain A- Hydrophobic interactions: K:W.24, C:I.19, C:T.225, C:I.229, A:L.478
- Salt bridges: C:R.5, C:H.221, A:R.479
- Hydrogen bonds: A:L.478, A:R.479
CDL.3: 20 residues within 4Å:- 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 F: R.71
- Chain G: Y.29, G.33, N.36, V.37, R.40
- Ligands: CDL.4
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
- Salt bridges: C:K.227, D:K.223, D:K.223, D:R.224, D:K.231, G:R.40
- 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
CDL.4: 10 residues within 4Å:- Chain C: S.28, S.29, W.30, F.33
- Chain F: Q.72
- Chain G: R.40, T.41, C.44
- Ligands: CDL.3, PEE.6
10 PLIP interactions:2 interactions with chain F, 4 interactions with chain G, 4 interactions with chain C- Hydrogen bonds: F:Q.72, F:Q.72, C:S.28, C:S.29, C:S.29, C:W.30
- Hydrophobic interactions: G:T.41
- Salt bridges: G:R.40, G:R.40, G:R.40
CDL.14: 11 residues within 4Å:- Chain L: F.370, W.477, L.478, R.479
- Chain N: R.5, I.19, H.221, T.225, I.229
- Chain V: W.24
- Ligands: PEE.17
10 PLIP interactions:5 interactions with chain N, 1 interactions with chain V, 4 interactions with chain L- Hydrophobic interactions: N:I.19, N:T.225, N:I.229, V:W.24, L:L.478
- Salt bridges: N:R.5, N:H.221, L:R.479
- Hydrogen bonds: L:L.478, L:R.479
CDL.15: 20 residues within 4Å:- Chain N: S.29, N.32, F.33, L.36, K.227, L.230, G.231, L.234
- Chain O: P.217, Y.220, K.223, R.224, K.231
- Chain Q: R.71
- Chain R: Y.29, G.33, N.36, V.37, R.40
- Ligands: CDL.16
18 PLIP interactions:8 interactions with chain O, 3 interactions with chain N, 7 interactions with chain R- Hydrophobic interactions: O:P.217, O:Y.220, N:F.33, N:L.36
- Hydrogen bonds: O:Y.220, O:R.224, R:Y.29, R:Y.29, R:Y.29, R:N.36, R:R.40, R:R.40
- Salt bridges: O:K.223, O:K.223, O:R.224, O:K.231, N:K.227, R:R.40
CDL.16: 10 residues within 4Å:- Chain N: S.28, S.29, W.30, F.33
- Chain Q: Q.72
- Chain R: R.40, T.41, C.44
- Ligands: CDL.15, PEE.18
10 PLIP interactions:4 interactions with chain N, 2 interactions with chain Q, 4 interactions with chain R- Hydrogen bonds: N:S.28, N:S.29, N:S.29, N:W.30, Q:Q.72, Q:Q.72
- 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 D: M.222
- Chain E: Y.37, T.40
- 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 E, 4 interactions with chain J, 2 interactions with chain A, 2 interactions with chain C- Hydrogen bonds: E:T.40
- pi-Cation interactions: E:Y.37, J:F.20, A:F.476
- Hydrophobic interactions: J:A.21, J:I.24, J:V.25, C:A.232, C:L.233
- Salt bridges: A:D.451
PLX.19: 17 residues within 4Å:- Chain L: D.451, F.476, L.478
- Chain N: A.232, L.233
- Chain O: M.222
- 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:4 interactions with chain U, 2 interactions with chain N, 2 interactions with chain L, 2 interactions with chain P- Hydrophobic interactions: U:A.21, U:I.24, U:V.25, N:A.232, N:L.233
- pi-Cation interactions: U:F.20, L:F.476, P:Y.37
- Salt bridges: L:D.451
- Hydrogen bonds: P:T.40
- 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
21 PLIP interactions:21 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: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
21 PLIP interactions:21 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: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
AL
AB
BM
BC
CN
CD
DO
DE
EP
EF
FQ
FG
GR
GH
HS
HI
IT
IJ
JU
JK
KV
K
- 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)
- 6 x CDL: CARDIOLIPIN(Non-covalent)
- 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)
- 6 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)
- 2 x FES: FE2/S2 (INORGANIC) CLUSTER(Non-covalent)
- 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)
- 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
AL
AB
BM
BC
CN
CD
DO
DE
EP
EF
FQ
FG
GR
GH
HS
HI
IT
IJ
JU
JK
KV
K