- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 3.48 Å
- Oligo State
- hetero-2-2-2-2-2-2-2-2-2-2-mer
- Ligands
- 6 x PEE: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine(Non-covalent)
- 5 x UNL: UNKNOWN LIGAND(Non-functional Binders)
UNL.2: 3 residues within 4Å:- Chain A: Q.430, L.431, L.432
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:Q.430
UNL.3: 2 residues within 4Å:- Chain A: H.271, N.274
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:N.274
UNL.12: 0 residues within 4Å:- (No contacts)
1 PLIP interactions:1 interactions with chain C- Hydrogen bonds: C:E.163
UNL.19: 1 residues within 4Å:- Chain K: H.360
No protein-ligand interaction detected (PLIP)UNL.31: 2 residues within 4Å:- Chain M: H.159, E.163
3 PLIP interactions:3 interactions with chain M- Hydrogen bonds: M:H.159, M:E.163, M:E.163
- 4 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)
HEM.4: 22 residues within 4Å:- Chain C: Q.45, I.46, G.49, L.50, L.52, A.53, Y.56, V.67, R.81, H.84, A.85, L.124, T.127, A.128, G.131, Y.132, L.134, P.135, H.183, F.184, P.187, I.190
20 PLIP interactions:20 interactions with chain C,- Hydrophobic interactions: C:Q.45, C:I.46, C:L.50, C:L.52, C:A.53, C:Y.56, C:V.67, C:L.124, C:T.127, C:L.134, C:L.134, C:F.184, C:I.190
- Water bridges: C:A.85
- Salt bridges: C:R.81, C:R.81
- pi-Stacking: C:H.84, C:H.183
- Metal complexes: C:H.84, C:H.183
HEM.5: 23 residues within 4Å:- Chain C: W.32, G.35, S.36, L.38, A.39, I.95, H.98, I.99, R.101, S.107, T.113, W.114, G.117, V.118, L.120, L.121, T.194, H.197, L.198, L.201, S.206, N.207
- Ligands: UQ.7
25 PLIP interactions:25 interactions with chain C,- Hydrophobic interactions: C:L.38, C:L.38, C:I.95, C:I.99, C:T.113, C:W.114, C:W.114, C:V.118, C:L.120, C:L.120, C:L.121, C:T.194, C:L.198, C:L.201
- Hydrogen bonds: C:W.32, C:G.35, C:N.207
- Water bridges: C:W.32, C:S.206
- Salt bridges: C:H.98, C:R.101, C:R.101
- pi-Stacking: C:H.98
- Metal complexes: C:H.98, C:H.197
HEM.20: 22 residues within 4Å:- Chain M: Q.45, I.46, G.49, L.50, L.52, A.53, Y.56, V.67, R.81, H.84, A.85, L.124, T.127, A.128, G.131, Y.132, L.134, P.135, H.183, F.184, P.187, I.190
20 PLIP interactions:20 interactions with chain M,- Hydrophobic interactions: M:Q.45, M:I.46, M:L.50, M:L.52, M:Y.56, M:V.67, M:A.85, M:L.124, M:T.127, M:A.128, M:L.134, M:L.134, M:F.184, M:P.187, M:I.190
- Water bridges: M:A.85
- Salt bridges: M:R.81, M:R.81
- Metal complexes: M:H.84, M:H.183
HEM.21: 23 residues within 4Å:- Chain M: W.32, G.35, S.36, L.38, A.39, I.95, H.98, I.99, R.101, S.107, T.113, W.114, G.117, V.118, L.120, L.121, T.194, H.197, L.198, L.201, S.206, N.207
- Ligands: UQ.24
21 PLIP interactions:21 interactions with chain M,- Hydrophobic interactions: M:L.38, M:L.38, M:I.95, M:I.99, M:T.113, M:W.114, M:W.114, M:V.118, M:L.120, M:L.121, M:L.198, M:L.201
- Hydrogen bonds: M:W.32, M:G.35, M:S.206, M:N.207
- Salt bridges: M:H.98, M:R.101, M:R.101
- Metal complexes: M:H.98, M:H.197
- 2 x IKR: methyl (2E)-{2-[(4-iodo-2,5-dimethylphenoxy)methyl]phenyl}(methoxyimino)ethanoate(Non-covalent)
IKR.6: 17 residues within 4Å:- Chain C: M.125, 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.295
12 PLIP interactions:12 interactions with chain C- Hydrophobic interactions: C:F.129, C:F.129, C:Y.132, C:I.269, C:P.271, C:F.275, C:F.275, C:A.278, C:Y.279, C:L.295
- Hydrogen bonds: C:E.272
- pi-Stacking: C:F.275
IKR.23: 16 residues within 4Å:- Chain M: M.125, 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, Y.279, L.295
12 PLIP interactions:12 interactions with chain M- Hydrophobic interactions: M:F.129, M:F.129, M:Y.132, M:I.147, M:I.269, M:P.271, M:F.275, M:F.275, M:Y.279, M:L.295
- 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.7: 15 residues within 4Å:- Chain C: S.18, L.19, L.22, P.23, A.24, I.28, S.36, A.39, L.198, L.201, H.202, S.206, F.221, D.229
- Ligands: HEM.5
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
UQ.24: 15 residues within 4Å:- Chain M: S.18, L.19, L.22, P.23, A.24, I.28, S.36, L.198, L.201, H.202, S.206, F.221, Y.225, D.229
- Ligands: HEM.21
4 PLIP interactions:4 interactions with chain M- Hydrophobic interactions: M:L.19, M:L.198, M:F.221
- Hydrogen bonds: M:S.206
- 4 x CDL: CARDIOLIPIN(Non-covalent)
CDL.8: 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.9, CDL.14
10 PLIP interactions:5 interactions with chain C, 4 interactions with chain G, 1 interactions with chain F- Hydrophobic interactions: C:W.31, G:V.37
- Hydrogen bonds: C:S.29, C:A.30, C:Y.105, C:Y.105
- Salt bridges: G:R.40, G:R.40, G:R.40, F:H.72
CDL.14: 12 residues within 4Å:- Chain C: A.30, N.33, K.228, G.232, L.235
- Chain D: Y.220, K.223, R.224
- Chain F: H.72, R.73
- Chain G: R.40
- Ligands: CDL.8
10 PLIP interactions:1 interactions with chain F, 2 interactions with chain G, 3 interactions with chain D, 4 interactions with chain C- Salt bridges: F:R.73, G:R.40, D:K.223, D:K.231, C:K.228, C:K.228
- Hydrogen bonds: G:R.40, D:R.224, C:N.33
- Hydrophobic interactions: C:A.30
CDL.25: 11 residues within 4Å:- Chain M: S.29, A.30, W.31, Y.105
- Chain P: H.72
- Chain Q: V.37, R.40, F.41, Q.44
- Ligands: PEE.26, CDL.33
11 PLIP interactions:5 interactions with chain M, 5 interactions with chain Q, 1 interactions with chain P- Hydrophobic interactions: M:W.31, Q:V.37, Q:Q.44
- 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
CDL.33: 14 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: I.29, R.40
- Ligands: CDL.25
13 PLIP interactions:6 interactions with chain N, 5 interactions with chain M, 1 interactions with chain P, 1 interactions with chain Q- Hydrophobic interactions: N:Y.220, N:Y.220, M:A.30, M:L.235
- Hydrogen bonds: N:Y.220, M:N.33, Q:R.40
- Salt bridges: N:K.223, N:R.224, N:K.231, M:K.228, M:K.228, P:R.73
- 2 x ZN: ZINC ION(Non-covalent)
ZN.10: 5 residues within 4Å:- Chain C: D.253, P.254, E.255, H.268
- Chain D: H.121
5 PLIP interactions:4 interactions with chain C, 1 interactions with chain D- Metal complexes: C:D.253, C:D.253, C:E.255, C:H.268, D:H.121
ZN.28: 5 residues within 4Å:- Chain M: D.253, P.254, E.255, H.268
- Chain N: H.121
4 PLIP interactions:3 interactions with chain M, 1 interactions with chain N- Metal complexes: M:D.253, M:E.255, M:H.268, N:H.121
- 2 x GOL: GLYCEROL(Non-functional Binders)
GOL.11: 7 residues within 4Å:- Chain C: F.64, V.67, R.81, P.135, N.256, F.257
- Chain D: Y.115
4 PLIP interactions:3 interactions with chain C, 1 interactions with chain D- Hydrogen bonds: C:R.81, C:R.81, C:N.256, D:Y.115
GOL.30: 8 residues within 4Å:- Chain M: F.64, V.67, A.68, C.71, R.81, N.256, F.257
- Chain N: Y.115
3 PLIP interactions:2 interactions with chain M, 1 interactions with chain N- Hydrogen bonds: M:R.81, M:R.81, N:Y.115
- 2 x HEC: HEME C(Covalent)
HEC.13: 20 residues within 4Å:- Chain D: V.32, V.36, C.37, A.39, C.40, H.41, N.105, A.108, P.110, P.111, R.120, Y.126, V.127, L.130, L.131, F.153, I.158, G.159, M.160, P.163
13 PLIP interactions:13 interactions with chain D,- Hydrophobic interactions: D:V.32, D:A.39, D:A.108, D:P.110, D:V.127, D:L.130, D:L.131, D:I.158, D:M.160, D:P.163
- Hydrogen bonds: D:G.159
- Salt bridges: D:R.120
- Metal complexes: D:H.41
HEC.32: 22 residues within 4Å:- Chain N: V.32, V.36, C.37, A.39, C.40, H.41, N.105, A.108, L.109, P.110, P.111, R.120, Y.126, V.127, L.130, L.131, F.153, I.158, G.159, M.160, P.163, V.186
16 PLIP interactions:16 interactions with chain N,- Hydrophobic interactions: N:V.32, N:A.39, N:A.108, N:P.110, N:V.127, N:L.130, N:L.131, N:I.158, N:M.160, N:P.163, N:V.186
- Hydrogen bonds: N:Y.126, N:G.159
- Salt bridges: N:R.120
- pi-Stacking: N:H.41
- Metal complexes: N:H.41
- 5 x BOG: octyl beta-D-glucopyranoside(Non-covalent)
BOG.15: 12 residues within 4Å:- Chain C: Y.76
- Chain D: Q.200, R.203, M.204, K.207, M.208
- Chain E: Y.49, A.50, N.53, Q.57
- Chain J: D.37
- Ligands: BOG.16
6 PLIP interactions:2 interactions with chain D, 1 interactions with chain J, 1 interactions with chain C, 2 interactions with chain E- Hydrogen bonds: D:Q.200, J:D.37, C:Y.76, E:N.53
- Salt bridges: D:K.207
- Hydrophobic interactions: E:Y.49
BOG.16: 3 residues within 4Å:- Chain D: Q.200, R.203
- Ligands: BOG.15
4 PLIP interactions:4 interactions with chain D- Hydrogen bonds: D:Q.200, D:R.203, D:R.203
- Salt bridges: D:R.203
BOG.22: 4 residues within 4Å:- Chain M: M.14, L.198, T.199, H.202
3 PLIP interactions:3 interactions with chain M- Hydrogen bonds: M:L.198, M:L.198
- Salt bridges: M:H.202
BOG.29: 3 residues within 4Å:- Chain M: Y.76
- Chain N: Q.200
- Ligands: BOG.34
2 PLIP interactions:1 interactions with chain N, 1 interactions with chain M- Hydrogen bonds: N:Q.200, M:Y.76
BOG.34: 11 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
- Ligands: BOG.29
6 PLIP interactions:3 interactions with chain O, 2 interactions with chain N, 1 interactions with chain T- Hydrophobic interactions: O:Y.49
- Hydrogen bonds: O:Y.49, O:N.53, N:Q.200, T:D.37
- Salt bridges: N:K.207
- 2 x FES: FE2/S2 (INORGANIC) CLUSTER(Non-covalent)
FES.17: 7 residues within 4Å:- Chain E: C.139, H.141, L.142, C.144, C.158, 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.35: 8 residues within 4Å:- Chain O: C.139, H.141, L.142, G.143, C.144, C.158, 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
- Berry, E.A. et al., Crystallographic location of two Zn(2+)-binding sites in the avian cytochrome bc(1) complex. Biochim.Biophys.Acta (2000)
- Release Date
- 2009-04-28
- 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 3.48 Å
- Oligo State
- hetero-2-2-2-2-2-2-2-2-2-2-mer
- Ligands
- 6 x PEE: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine(Non-covalent)
- 5 x UNL: UNKNOWN LIGAND(Non-functional Binders)
- 4 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)
- 2 x IKR: methyl (2E)-{2-[(4-iodo-2,5-dimethylphenoxy)methyl]phenyl}(methoxyimino)ethanoate(Non-covalent)
- 2 x UQ: Coenzyme Q10, (2Z,6E,10Z,14E,18E,22E,26Z)-isomer(Non-covalent)
- 4 x CDL: CARDIOLIPIN(Non-covalent)
- 2 x ZN: ZINC ION(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
- Berry, E.A. et al., Crystallographic location of two Zn(2+)-binding sites in the avian cytochrome bc(1) complex. Biochim.Biophys.Acta (2000)
- Release Date
- 2009-04-28
- 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.