- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 3.23 Å
- Oligo State
- hetero-2-2-2-2-2-2-2-2-2-2-mer
- Ligands
- 14 x PEE: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine(Non-covalent)
- 4 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)
HEM.2: 23 residues within 4Å:- Chain C: L.42, Q.45, I.46, G.49, L.50, L.52, A.53, Y.56, R.81, H.84, A.88, F.91, L.124, T.127, A.128, G.131, Y.132, L.134, P.135, H.183, F.184, P.187, Y.274
16 PLIP interactions:16 interactions with chain C,- Hydrophobic interactions: C:L.42, C:Q.45, C:L.50, C:L.52, C:L.52, C:A.53, C:Y.56, C:F.91, C:T.127, C:L.134, C:L.134, C:F.184
- Salt bridges: C:R.81, C:R.81
- Metal complexes: C:H.84, C:H.183
HEM.3: 25 residues within 4Å:- Chain C: W.32, G.35, S.36, L.38, A.39, F.91, I.95, H.98, I.99, R.101, S.107, T.113, W.114, G.117, V.118, L.120, L.121, I.190, T.194, H.197, L.198, L.201, S.206, N.207
- Ligands: U10.5
23 PLIP interactions:23 interactions with chain C,- Hydrophobic interactions: C:L.38, C:L.38, C:F.91, C:I.95, C:T.113, C:W.114, C:W.114, C:W.114, C:L.120, C:L.121, C:I.190, C:T.194, C:L.198, C:L.201, C:L.201
- Hydrogen bonds: C:G.35, C:S.206, C:N.207
- Salt bridges: C:H.98, C:R.101, C:R.101
- Metal complexes: C:H.98, C:H.197
HEM.21: 23 residues within 4Å:- Chain M: L.42, Q.45, I.46, G.49, L.50, L.52, A.53, Y.56, R.81, H.84, A.88, F.91, L.124, T.127, A.128, G.131, Y.132, L.134, P.135, H.183, F.184, P.187, Y.274
16 PLIP interactions:16 interactions with chain M,- Hydrophobic interactions: M:L.42, M:Q.45, M:L.50, M:L.52, M:L.52, M:A.53, M:Y.56, M:F.91, M:T.127, M:L.134, M:L.134, M:F.184
- Salt bridges: M:R.81, M:R.81
- Metal complexes: M:H.84, M:H.183
HEM.22: 25 residues within 4Å:- Chain M: W.32, G.35, S.36, L.38, A.39, F.91, I.95, H.98, I.99, R.101, S.107, T.113, W.114, G.117, V.118, L.120, L.121, I.190, T.194, H.197, L.198, L.201, S.206, N.207
- Ligands: U10.24
24 PLIP interactions:24 interactions with chain M,- Hydrophobic interactions: M:L.38, M:L.38, M:F.91, M:I.95, M:T.113, M:W.114, M:W.114, M:W.114, M:L.120, M:L.121, M:I.190, M:T.194, M:L.198, M:L.201, M:L.201
- Hydrogen bonds: M:G.35, M:S.206, M:N.207
- Water bridges: M:S.36
- Salt bridges: M:H.98, M:R.101, M:R.101
- Metal complexes: M:H.98, M:H.197
- 2 x Y52: methyl (2E)-3-methoxy-2-(2-{[(5-methoxy-1,3-benzothiazol-2-yl)sulfanyl]methyl}phenyl)prop-2-enoate(Non-covalent)
Y52.4: 21 residues within 4Å:- Chain C: L.122, M.125, A.126, A.128, F.129, Y.132, V.133, M.139, S.140, G.143, A.144, I.147, I.269, K.270, P.271, E.272, Y.274, F.275, Y.279, L.295
- Ligands: PEE.10
9 PLIP interactions:9 interactions with chain C- Hydrophobic interactions: C:F.129, C:Y.132, C:I.147, C:I.269, C:P.271, C:Y.279
- Hydrogen bonds: C:E.272
- pi-Stacking: C:F.275, C:F.275
Y52.23: 19 residues within 4Å:- Chain M: L.122, M.125, A.126, A.128, F.129, Y.132, V.133, S.140, G.143, A.144, I.147, K.270, P.271, E.272, Y.274, F.275, Y.279, L.295
- Ligands: PEE.28
9 PLIP interactions:9 interactions with chain M- Hydrophobic interactions: M:M.125, M:F.129, M:Y.132, M:I.147, M:P.271, M:Y.279
- Hydrogen bonds: M:E.272
- pi-Stacking: M:F.275, M:F.275
- 2 x U10: UBIQUINONE-10(Non-covalent)
U10.5: 14 residues within 4Å:- Chain C: S.18, L.19, L.22, A.24, I.28, S.36, A.39, L.198, H.202, S.206, F.221, Y.225, D.229
- Ligands: HEM.3
5 PLIP interactions:5 interactions with chain C- Hydrophobic interactions: C:L.19, C:A.39, C:L.198, C:F.221
- Hydrogen bonds: C:S.206
U10.24: 16 residues within 4Å:- Chain M: S.18, L.19, L.22, A.24, I.28, S.36, A.39, L.198, L.201, H.202, S.206, F.221, Y.225, D.229
- Ligands: PEE.20, HEM.22
6 PLIP interactions:6 interactions with chain M- Hydrophobic interactions: M:L.19, M:A.39, M:L.198, M:F.221
- Hydrogen bonds: M:S.206
- pi-Stacking: M:F.221
- 1 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)
- 2 x GOL: GLYCEROL(Non-functional Binders)
GOL.9: 5 residues within 4Å:- Chain C: F.64, R.81, N.256, F.257
- Chain D: Y.115
5 PLIP interactions:4 interactions with chain C, 1 interactions with chain D- Hydrogen bonds: C:F.64, C:R.81, C:R.81, C:N.256, D:Y.115
GOL.27: 5 residues within 4Å:- Chain M: F.64, R.81, N.256, F.257
- Chain N: Y.115
5 PLIP interactions:4 interactions with chain M, 1 interactions with chain N- Hydrogen bonds: M:F.64, M:R.81, M:R.81, M:N.256, N:Y.115
- 2 x HEC: HEME C(Covalent)
HEC.12: 21 residues within 4Å:- Chain D: V.32, V.36, C.37, C.40, H.41, N.105, A.108, P.110, P.111, I.116, R.120, Y.126, L.130, L.131, F.153, I.158, G.159, M.160, P.163, I.164, V.186
18 PLIP interactions:18 interactions with chain D,- Hydrophobic interactions: D:V.32, D:V.36, D:N.105, D:A.108, D:P.110, D:P.111, D:I.116, D:L.130, D:L.131, D:I.158, D:M.160, D:P.163, D:I.164, D:V.186
- Hydrogen bonds: D:Y.126, D:G.159
- Salt bridges: D:R.120
- Metal complexes: D:H.41
HEC.31: 21 residues within 4Å:- Chain N: V.32, V.36, C.37, C.40, H.41, N.105, A.108, P.110, P.111, I.116, R.120, Y.126, L.130, L.131, F.153, I.158, G.159, M.160, P.163, I.164, V.186
19 PLIP interactions:19 interactions with chain N,- Hydrophobic interactions: N:V.32, N:V.36, N:N.105, N:A.108, N:P.110, N:P.111, N:I.116, N:L.130, N:L.131, N:I.158, N:M.160, N:P.163, N:I.164, N:V.186
- Hydrogen bonds: N:Y.126, N:Y.126, N:G.159
- Salt bridges: N:R.120
- Metal complexes: N:H.41
- 4 x CDL: CARDIOLIPIN(Non-covalent)
CDL.13: 17 residues within 4Å:- Chain C: A.30, N.33, K.228, L.231, G.232, L.235, M.236
- Chain D: Y.220, K.223, R.224, K.231
- Chain F: H.72, R.73
- Chain G: I.29, A.33, V.37
- Ligands: CDL.18
5 PLIP interactions:1 interactions with chain F, 3 interactions with chain D, 1 interactions with chain C- Salt bridges: F:R.73, D:K.223, D:R.224, C:K.228
- Hydrophobic interactions: D:Y.220
CDL.18: 11 residues within 4Å:- Chain C: S.29, A.30, W.31, Y.105
- Chain F: H.72
- Chain G: V.37, R.40, F.41, Q.44
- Ligands: PEE.6, CDL.13
10 PLIP interactions:4 interactions with chain C, 5 interactions with chain G, 1 interactions with chain F- Hydrophobic interactions: C:W.31, G:F.41, G:F.41
- Hydrogen bonds: C:S.29, C:A.30, C:Y.105
- Salt bridges: G:R.40, G:R.40, G:R.40, F:H.72
CDL.32: 15 residues within 4Å:- Chain M: A.30, N.33, K.228, G.232, L.235, M.236
- Chain N: Y.220, K.223, R.224
- Chain P: H.72, R.73
- Chain Q: I.29, A.33, V.37
- Ligands: CDL.36
7 PLIP interactions:1 interactions with chain P, 5 interactions with chain N, 1 interactions with chain M- Hydrogen bonds: P:R.73, N:Y.220
- Hydrophobic interactions: N:Y.220, N:Y.220
- Salt bridges: N:K.223, N:R.224, M:K.228
CDL.36: 14 residues within 4Å:- Chain M: S.29, A.30, W.31, F.34, Y.105
- Chain P: H.72
- Chain Q: V.37, R.40, F.41, Q.44, V.45, V.48
- Ligands: PEE.26, CDL.32
12 PLIP interactions:6 interactions with chain M, 5 interactions with chain Q, 1 interactions with chain P- Hydrophobic interactions: M:W.31, M:F.34, Q:F.41, Q:V.48
- Hydrogen bonds: M:S.29, M:A.30, M:Y.105, M:Y.105
- Salt bridges: Q:R.40, Q:R.40, Q:R.40, P:H.72
- 3 x BOG: octyl beta-D-glucopyranoside(Non-covalent)
BOG.14: 12 residues within 4Å:- Chain C: Y.76, L.241
- Chain D: Q.200, R.203, M.204, K.207, M.208, I.211
- Chain E: A.50, N.53, Q.57
- Ligands: PEE.17
9 PLIP interactions:4 interactions with chain D, 3 interactions with chain E, 2 interactions with chain C- Hydrophobic interactions: D:I.211, E:A.50, C:L.241
- Hydrogen bonds: D:Q.200, D:R.203, E:N.53, E:Q.57, C:Y.76
- Salt bridges: D:K.207
BOG.25: 8 residues within 4Å:- Chain M: V.40, T.44, I.230, L.233, L.237, L.241
- Chain O: V.54
- Ligands: PEE.35
4 PLIP interactions:1 interactions with chain O, 3 interactions with chain M- Hydrophobic interactions: O:V.54, M:V.40, M:L.237, M:L.241
BOG.33: 10 residues within 4Å:- Chain M: Y.76
- Chain N: Q.200, R.203, M.204, K.207, M.208, I.211
- Chain O: A.50, N.53, Q.57
6 PLIP interactions:4 interactions with chain N, 2 interactions with chain O- Hydrophobic interactions: N:K.207, N:I.211
- Hydrogen bonds: N:Q.200, O:N.53, O:Q.57
- Salt bridges: N:K.207
- 2 x FES: FE2/S2 (INORGANIC) CLUSTER(Non-covalent)
FES.15: 7 residues within 4Å:- Chain E: C.139, H.141, L.142, C.158, C.160, H.161, S.163
4 PLIP interactions:4 interactions with chain E,- Metal complexes: E:C.139, E:H.141, E:C.158, E:H.161
FES.34: 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., Rational Design of Highly Potent and Slow-Binding Cytochrome bc1 Inhibitor as Fungicide by Computational Substitution Optimization. Sci Rep (2015)
- Release Date
- 2015-07-29
- 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
Cytochrome b-c1 complex subunit 7: FP
Mitochondrial ubiquinol-cytochrome c reductase ubiquinone-binding protein qp-c: GQ
Cytochrome b-c1 complex subunit 6: 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 3.23 Å
- Oligo State
- hetero-2-2-2-2-2-2-2-2-2-2-mer
- Ligands
- 14 x PEE: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine(Non-covalent)
- 4 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)
- 2 x Y52: methyl (2E)-3-methoxy-2-(2-{[(5-methoxy-1,3-benzothiazol-2-yl)sulfanyl]methyl}phenyl)prop-2-enoate(Non-covalent)
- 2 x U10: UBIQUINONE-10(Non-covalent)
- 1 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)
- 2 x GOL: GLYCEROL(Non-functional Binders)
- 2 x HEC: HEME C(Covalent)
- 4 x CDL: CARDIOLIPIN(Non-covalent)
- 3 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., Rational Design of Highly Potent and Slow-Binding Cytochrome bc1 Inhibitor as Fungicide by Computational Substitution Optimization. Sci Rep (2015)
- Release Date
- 2015-07-29
- 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
Cytochrome b-c1 complex subunit 7: FP
Mitochondrial ubiquinol-cytochrome c reductase ubiquinone-binding protein qp-c: GQ
Cytochrome b-c1 complex subunit 6: 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.