- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.70 Å
- Oligo State
- hetero-2-2-2-2-2-2-2-2-2-2-mer
- Ligands
- 2 x UNL: UNKNOWN LIGAND
- 4 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)
- 2 x WF3: methyl (2E)-3-methoxy-2-[2-({[6-methyl-3-(trifluoromethyl)quinoxalin-2-yl]oxy}methyl)phenyl]prop-2-enoate(Non-covalent)
WF3.4: 19 residues within 4Å:- Chain C: M.125, A.128, F.129, Y.132, V.133, S.140, G.143, A.144, I.147, I.269, K.270, P.271, E.272, Y.274, F.275, A.278, Y.279, L.282, L.295
9 PLIP interactions:9 interactions with chain C- Hydrophobic interactions: C:M.125, C:F.129, C:Y.132, C:I.147, C:I.269, C:P.271, C:F.275
- Hydrogen bonds: C:E.272
- pi-Stacking: C:F.275
WF3.21: 17 residues within 4Å:- Chain M: M.125, A.128, F.129, Y.132, V.133, G.143, A.144, I.147, K.270, P.271, E.272, Y.274, F.275, A.278, Y.279, L.282, L.295
8 PLIP interactions:8 interactions with chain M- Hydrophobic interactions: M:M.125, M:F.129, M:Y.132, M:I.147, M:P.271, M:F.275
- Hydrogen bonds: M:E.272
- pi-Stacking: M:F.275
- 2 x UQ: Coenzyme Q10, (2Z,6E,10Z,14E,18E,22E,26Z)-isomer(Non-covalent)
UQ.5: 12 residues within 4Å:- Chain C: S.18, L.19, L.22, I.28, A.39, L.198, L.201, H.202, S.206, F.221, D.229
- Ligands: HEM.3
4 PLIP interactions:4 interactions with chain C- Hydrophobic interactions: C:A.39, C:L.198, C:F.221
- Hydrogen bonds: C:S.206
UQ.22: 13 residues within 4Å:- Chain M: S.18, L.19, L.22, I.28, A.39, L.198, L.201, H.202, S.206, F.221, Y.225, D.229
- Ligands: HEM.19
3 PLIP interactions:3 interactions with chain M- Hydrophobic interactions: M:A.39, M:L.198, M:F.221
- 4 x CDL: CARDIOLIPIN(Non-covalent)
CDL.6: 13 residues within 4Å:- Chain C: A.30, N.33, K.228, G.232, L.235
- Chain D: Y.220, K.223, R.224, K.231
- Chain F: H.72, R.73
- Chain G: R.40
- Ligands: CDL.15
9 PLIP interactions:4 interactions with chain D, 2 interactions with chain C, 1 interactions with chain F, 2 interactions with chain G- Hydrophobic interactions: D:Y.220, C:A.30
- Salt bridges: D:K.223, D:R.224, D:K.231, C:K.228, F:R.73, G:R.40
- Hydrogen bonds: G:R.40
CDL.15: 10 residues within 4Å:- Chain C: S.29, A.30, W.31, Y.105
- Chain F: H.72
- Chain G: R.40, F.41, Q.44
- Ligands: CDL.6, PEE.7
9 PLIP interactions:6 interactions with chain G, 1 interactions with chain F, 2 interactions with chain C- Hydrophobic interactions: G:F.41, G:F.41, G:Q.44, C:W.31
- Hydrogen bonds: G:R.40, C:A.30
- Salt bridges: G:R.40, G:R.40, F:H.72
CDL.23: 10 residues within 4Å:- Chain M: S.29, A.30, W.31, Y.105
- Chain P: H.72
- Chain Q: R.40, F.41, Q.44
- Ligands: PEE.24, CDL.27
9 PLIP interactions:1 interactions with chain P, 3 interactions with chain M, 5 interactions with chain Q- Salt bridges: P:H.72, Q:R.40, Q:R.40
- Hydrophobic interactions: M:W.31, Q:F.41, Q:Q.44
- Hydrogen bonds: M:A.30, M:Y.105, Q:R.40
CDL.27: 13 residues within 4Å:- Chain M: A.30, N.33, K.228, G.232, L.235
- Chain N: Y.220, K.223, R.224, K.231
- Chain P: H.72, R.73
- Chain Q: R.40
- Ligands: CDL.23
10 PLIP interactions:5 interactions with chain N, 1 interactions with chain P, 2 interactions with chain M, 2 interactions with chain Q- Hydrophobic interactions: N:Y.220, N:Y.220, M:A.30
- Salt bridges: N:K.223, N:R.224, N:K.231, P:R.73, M:K.228, Q:R.40
- Hydrogen bonds: Q:R.40
- 6 x PEE: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine(Non-covalent)
PEE.7: 16 residues within 4Å:- Chain C: W.31, F.96, L.97, Y.104, Y.105, F.277, T.317, F.326, W.327, L.333, L.334
- Chain F: Y.29
- Chain G: R.40, Q.44, V.48
- Ligands: CDL.15
14 PLIP interactions:14 interactions with chain C- Hydrophobic interactions: C:W.31, C:W.31, C:F.96, C:F.96, C:L.97, C:Y.104, C:Y.104, C:Y.105, C:F.277, C:F.326, C:W.327
- Hydrogen bonds: C:Y.104, C:Y.104, C:Y.105
PEE.8: 6 residues within 4Å:- Chain A: S.439, Y.442, W.443
- Chain C: H.222, I.230
- Ligands: PEE.14
2 PLIP interactions:2 interactions with chain C- Hydrophobic interactions: C:I.230
- Salt bridges: C:H.222
PEE.14: 16 residues within 4Å:- Chain A: Y.442
- Chain C: F.227, I.230
- Chain D: M.222
- Chain E: Y.37, T.40, T.47, A.48, A.50, A.51, K.52
- Chain J: F.11, A.18, V.21, E.29
- Ligands: PEE.8
11 PLIP interactions:5 interactions with chain E, 1 interactions with chain D, 3 interactions with chain J, 1 interactions with chain C, 1 interactions with chain A- Hydrophobic interactions: E:T.47, E:A.48, E:A.50, E:A.51, E:K.52, J:A.18, J:V.21, C:I.230
- Salt bridges: D:K.226
- Hydrogen bonds: J:F.11, A:Y.442
PEE.17: 4 residues within 4Å:- Chain K: S.439, Y.442
- Chain M: H.222
- Ligands: PEE.31
3 PLIP interactions:1 interactions with chain M, 2 interactions with chain K- Salt bridges: M:H.222
- Hydrogen bonds: K:S.439, K:Y.442
PEE.24: 17 residues within 4Å:- Chain M: W.31, F.96, L.97, Y.104, Y.105, F.277, T.317, F.326, W.327, L.333, L.334, T.337
- Chain P: Y.29
- Chain Q: Q.44, V.48, F.52
- Ligands: CDL.23
15 PLIP interactions:14 interactions with chain M, 1 interactions with chain Q- Hydrophobic interactions: M:W.31, M:W.31, M:F.96, M:L.97, M:Y.104, M:Y.104, M:Y.105, M:F.277, M:F.277, M:F.326, M:W.327, M:W.327, Q:F.52
- Hydrogen bonds: M:Y.104, M:Y.105
PEE.31: 20 residues within 4Å:- Chain K: Y.442
- Chain M: F.227, I.230, L.241
- Chain N: M.204, M.222
- Chain O: Y.37, T.40, C.44, T.47, A.48, K.52, V.54, Q.57
- Chain T: F.11, R.12, V.21, V.22, E.29
- Ligands: PEE.17
10 PLIP interactions:5 interactions with chain O, 2 interactions with chain T, 2 interactions with chain M, 1 interactions with chain N- Hydrophobic interactions: O:T.47, O:A.48, O:V.54, T:V.21, T:V.22, M:L.241, M:L.241
- Hydrogen bonds: O:Y.37, O:T.40
- Salt bridges: N:K.226
- 2 x GOL: GLYCEROL(Non-functional Binders)
GOL.9: 6 residues within 4Å:- Chain C: F.64, R.81, P.135, N.256, F.257
- Chain D: Y.115
4 PLIP interactions:1 interactions with chain D, 3 interactions with chain C- Hydrogen bonds: D:Y.115, C:R.81, C:R.81, C:N.256
GOL.25: 8 residues within 4Å:- Chain M: F.64, V.67, A.68, R.81, P.135, N.256, F.257
- Chain N: Y.115
4 PLIP interactions:3 interactions with chain M, 1 interactions with chain N- Hydrogen bonds: M:R.81, M:R.81, M:P.135, N:Y.115
- 2 x HEC: HEME C(Covalent)
HEC.10: 20 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, I.116, R.120, Y.126, L.131, F.153, I.158, G.159, M.160, P.163, I.164
15 PLIP interactions:15 interactions with chain D,- Hydrophobic interactions: D:V.32, D:N.105, D:A.108, D:P.110, D:I.116, D:L.131, D:I.158, D:M.160, D:P.163, D:I.164
- Hydrogen bonds: D:G.159
- Salt bridges: D:R.120
- pi-Stacking: D:H.41, D:H.41
- Metal complexes: D:H.41
HEC.26: 20 residues within 4Å:- Chain N: V.32, V.36, C.37, C.40, H.41, N.105, A.108, L.109, P.110, P.111, I.116, R.120, Y.126, L.131, F.153, I.158, G.159, M.160, P.163, I.164
16 PLIP interactions:16 interactions with chain N,- Hydrophobic interactions: N:V.32, N:N.105, N:A.108, N:P.110, N:I.116, N:L.131, N:I.158, N:M.160, N:P.163, N:I.164
- Hydrogen bonds: N:Y.126, N:G.159
- Salt bridges: N:R.120
- pi-Stacking: N:H.41, N:H.41
- Metal complexes: N:H.41
- 5 x BOG: octyl beta-D-glucopyranoside(Non-covalent)
BOG.11: 11 residues within 4Å:- Chain C: Y.76
- Chain D: Q.200, R.203, M.204, K.207
- Chain E: Y.49, A.50, N.53, Q.57
- Chain J: D.37
- Ligands: BOG.12
8 PLIP interactions:3 interactions with chain E, 2 interactions with chain D, 2 interactions with chain C, 1 interactions with chain J- Hydrophobic interactions: E:Y.49, E:A.50
- Hydrogen bonds: E:N.53, D:Q.200, C:Y.76, C:Y.76, J:D.37
- Salt bridges: D:K.207
BOG.12: 3 residues within 4Å:- Chain D: Q.200, R.203
- Ligands: BOG.11
1 PLIP interactions:1 interactions with chain D- Hydrogen bonds: D:R.203
BOG.20: 6 residues within 4Å:- Chain M: M.14, S.18, I.195, L.198, T.199, H.202
3 PLIP interactions:3 interactions with chain M- Hydrogen bonds: M:S.18, M:S.18
- Salt bridges: M:H.202
BOG.28: 12 residues within 4Å:- Chain M: Y.76
- Chain N: Q.200, R.203, M.204, K.207, M.208
- Chain O: Y.49, A.50, N.53, Q.57
- Chain T: D.37
- Ligands: BOG.29
7 PLIP interactions:3 interactions with chain O, 3 interactions with chain N, 1 interactions with chain T- Hydrophobic interactions: O:Y.49, O:A.50, N:K.207
- Hydrogen bonds: O:N.53, N:Q.200, T:D.37
- Salt bridges: N:K.207
BOG.29: 3 residues within 4Å:- Chain N: Q.200, R.203
- Ligands: BOG.28
No protein-ligand interaction detected (PLIP)- 2 x FES: FE2/S2 (INORGANIC) CLUSTER(Non-covalent)
FES.13: 10 residues within 4Å:- Chain E: C.139, H.141, L.142, C.144, C.158, C.160, H.161, G.162, S.163, P.175
4 PLIP interactions:4 interactions with chain E,- Metal complexes: E:C.139, E:H.141, E:C.158, E:H.161
FES.30: 8 residues within 4Å:- Chain O: C.139, H.141, L.142, C.144, C.158, C.160, H.161, S.163
4 PLIP interactions:4 interactions with chain O,- Metal complexes: O:C.139, O:H.141, O:C.158, O:H.161
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Hao, G.F. et al., Computational discovery of picomolar Q(o) site inhibitors of cytochrome bc1 complex. J.Am.Chem.Soc. (2012)
- Release Date
- 2012-07-04
- Peptides
- Mitochondrial ubiquinol-cytochrome-c reductase complex core protein i: AK
Mitochondrial ubiquinol-cytochrome-c reductase complex core protein 2: BL
Cytochrome b: CM
Mitochondrial cytochrome c1, heme protein: DN
Cytochrome b-c1 complex subunit Rieske, mitochondrial: EO
Mitochondrial ubiquinol-cytochrome c reductase 14 kda protein: FP
Mitochondrial ubiquinol-cytochrome c reductase ubiquinone-binding protein qp-c: GQ
Mitochondrial ubiquinol-cytochrome c reductase 11 kda protein, complex iii subunit viii: HR
Cytochrome b-c1 complex subunit Rieske, mitochondrial: IS
Mitochondrial ubiquinol-cytochrome c reductase 7.2 kda protein: JT - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AK
NB
BL
OC
CM
PD
DN
QE
EO
RF
FP
SG
GQ
TH
HR
UI
IS
VJ
JT
W - Membrane
-
We predict this structure to be a membrane protein.
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.70 Å
- Oligo State
- hetero-2-2-2-2-2-2-2-2-2-2-mer
- Ligands
- 2 x UNL: UNKNOWN LIGAND
- 4 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)
- 2 x WF3: methyl (2E)-3-methoxy-2-[2-({[6-methyl-3-(trifluoromethyl)quinoxalin-2-yl]oxy}methyl)phenyl]prop-2-enoate(Non-covalent)
- 2 x UQ: Coenzyme Q10, (2Z,6E,10Z,14E,18E,22E,26Z)-isomer(Non-covalent)
- 4 x CDL: CARDIOLIPIN(Non-covalent)
- 6 x PEE: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine(Non-covalent)
- 2 x GOL: GLYCEROL(Non-functional Binders)
- 2 x HEC: HEME C(Covalent)
- 5 x BOG: octyl beta-D-glucopyranoside(Non-covalent)
- 2 x FES: FE2/S2 (INORGANIC) CLUSTER(Non-covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Hao, G.F. et al., Computational discovery of picomolar Q(o) site inhibitors of cytochrome bc1 complex. J.Am.Chem.Soc. (2012)
- Release Date
- 2012-07-04
- Peptides
- Mitochondrial ubiquinol-cytochrome-c reductase complex core protein i: AK
Mitochondrial ubiquinol-cytochrome-c reductase complex core protein 2: BL
Cytochrome b: CM
Mitochondrial cytochrome c1, heme protein: DN
Cytochrome b-c1 complex subunit Rieske, mitochondrial: EO
Mitochondrial ubiquinol-cytochrome c reductase 14 kda protein: FP
Mitochondrial ubiquinol-cytochrome c reductase ubiquinone-binding protein qp-c: GQ
Mitochondrial ubiquinol-cytochrome c reductase 11 kda protein, complex iii subunit viii: HR
Cytochrome b-c1 complex subunit Rieske, mitochondrial: IS
Mitochondrial ubiquinol-cytochrome c reductase 7.2 kda protein: JT - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AK
NB
BL
OC
CM
PD
DN
QE
EO
RF
FP
SG
GQ
TH
HR
UI
IS
VJ
JT
W - Membrane
-
We predict this structure to be a membrane protein.