- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 3.21 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)
- 12 x UNL: UNKNOWN LIGAND
UNL.2: 3 residues within 4Å:- Chain A: G.285, G.286
- Chain B: S.84
2 PLIP interactions:1 interactions with chain B, 1 interactions with chain A- Hydrogen bonds: B:S.84, A:G.286
UNL.9: 3 residues within 4Å:- Chain C: F.129, Y.132
- Ligands: 3H1.5
No protein-ligand interaction detected (PLIP)UNL.10: 2 residues within 4Å:- Chain C: N.149
- Ligands: UNL.35
1 PLIP interactions:1 interactions with chain C- Hydrogen bonds: C:N.149
UNL.11: 2 residues within 4Å:- Chain C: T.199, H.202
2 PLIP interactions:2 interactions with chain C- Hydrogen bonds: C:T.199, C:T.199
UNL.12: 1 residues within 4Å:- Chain C: L.250
1 PLIP interactions:1 interactions with chain C- Hydrogen bonds: C:L.250
UNL.18: 1 residues within 4Å:- Chain E: Y.178
No protein-ligand interaction detected (PLIP)UNL.22: 1 residues within 4Å:- Chain M: T.199
1 PLIP interactions:1 interactions with chain M- Hydrogen bonds: M:T.199
UNL.23: 2 residues within 4Å:- Chain M: L.250, G.252
1 PLIP interactions:1 interactions with chain M- Hydrogen bonds: M:L.250
UNL.29: 3 residues within 4Å:- Chain M: A.85, S.89, Y.274
No protein-ligand interaction detected (PLIP)UNL.30: 2 residues within 4Å:- Chain M: N.149
- Ligands: UNL.31
2 PLIP interactions:1 interactions with chain M, 1 interactions with chain E- Hydrogen bonds: M:N.149, E:T.140
UNL.31: 4 residues within 4Å:- Chain M: N.149, V.162, W.166
- Ligands: UNL.30
2 PLIP interactions:2 interactions with chain M- Hydrogen bonds: M:N.149, M:H.159
UNL.35: 4 residues within 4Å:- Chain C: N.149
- Chain O: C.139, T.140
- Ligands: UNL.10
3 PLIP interactions:2 interactions with chain O, 1 interactions with chain C- Hydrogen bonds: O:C.139, O:G.143, C:N.149
- 4 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)
HEM.3: 23 residues within 4Å:- Chain C: Q.45, G.49, L.50, L.52, A.53, Y.56, V.67, R.81, H.84, A.85, A.88, L.124, T.127, A.128, G.131, Y.132, L.134, P.135, H.183, F.184, P.187, I.190, Y.274
17 PLIP interactions:17 interactions with chain C,- Hydrophobic interactions: C:Q.45, C:L.50, C:L.52, C:A.53, C:Y.56, C:V.67, C:A.85, C:A.88, C:L.124, C:T.127, C:L.134, C:F.184, C:I.190
- Salt bridges: C:R.81, C:R.81
- Metal complexes: C:H.84, C:H.183
HEM.4: 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: 3H1.6
21 PLIP interactions:21 interactions with chain C,- Hydrophobic interactions: C:L.38, C:L.38, C:I.95, C:T.113, C:W.114, C:L.120, C:L.120, C:L.121, C:L.198, C:L.201, C:L.201
- Hydrogen bonds: C:G.35, C:S.206, C:N.207
- Water bridges: C:W.32, C:R.101
- Salt bridges: C:H.98, C:R.101, C:R.101
- Metal complexes: C:H.98, C:H.197
HEM.20: 23 residues within 4Å:- Chain M: Q.45, G.49, L.50, L.52, A.53, Y.56, V.67, R.81, H.84, A.85, A.88, L.124, T.127, A.128, G.131, Y.132, L.134, P.135, H.183, F.184, P.187, I.190, Y.274
16 PLIP interactions:16 interactions with chain M,- Hydrophobic interactions: M:Q.45, M:L.50, M:L.52, M:A.53, M:Y.56, M:A.85, M:A.88, M:L.124, M:T.127, M:L.134, M:F.184, M:I.190
- 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: 3H1.25
24 PLIP interactions:24 interactions with chain M,- Hydrophobic interactions: M:L.38, M:L.38, M:I.95, M:T.113, M:W.114, M:W.114, M:L.120, M:L.120, M:L.121, M:L.198, M:L.201, M:L.201
- Hydrogen bonds: M:G.35, M:N.207
- Water bridges: M:W.32, M:R.101
- Salt bridges: M:H.98, M:R.101, M:R.101
- pi-Stacking: M:H.98, M:H.98, M:H.197
- Metal complexes: M:H.98, M:H.197
- 4 x 3H1: 3-chloro-4,6-dihydroxy-2-methyl-5-{(2E,4E)-3-methyl-5-[(1R,2R,6R)-1,2,6-trimethyl-3-oxocyclohexyl]penta-2,4-dien-1-yl}benzaldehyde(Non-covalent)
3H1.5: 14 residues within 4Å:- Chain C: A.126, F.129, G.143, V.146, I.147, P.271, F.275, A.278, Y.279, L.282, L.295
- Chain O: C.160, H.161
- Ligands: UNL.9
6 PLIP interactions:5 interactions with chain C, 1 interactions with chain O- Hydrophobic interactions: C:F.129, C:F.275, C:A.278, C:Y.279, C:L.295
- Hydrogen bonds: O:H.161
3H1.6: 13 residues within 4Å:- Chain C: L.19, L.22, S.36, A.39, L.198, L.201, H.202, S.206, F.221, D.229, I.230
- Ligands: PEE.1, HEM.4
6 PLIP interactions:6 interactions with chain C- Hydrophobic interactions: C:L.19, C:L.19, C:A.39, C:I.230
- Water bridges: C:S.36
- pi-Stacking: C:F.221
3H1.24: 16 residues within 4Å:- Chain E: C.160, H.161
- Chain M: L.122, M.125, A.126, F.129, G.143, V.146, I.147, P.271, E.272, F.275, A.278, Y.279, L.282, L.295
8 PLIP interactions:7 interactions with chain M, 1 interactions with chain E- Hydrophobic interactions: M:L.122, M:F.129, M:F.275, M:F.275, M:A.278, M:L.295
- Halogen bonds: M:E.272
- Hydrogen bonds: E:H.161
3H1.25: 14 residues within 4Å:- Chain M: L.19, L.22, I.28, S.36, A.39, L.198, L.201, H.202, S.206, F.221, Y.225, D.229, I.230
- Ligands: HEM.21
8 PLIP interactions:8 interactions with chain M- Hydrophobic interactions: M:L.19, M:L.19, M:L.22, M:A.39, M:F.221, M:I.230
- Water bridges: M:W.32, M:D.229
- 4 x CDL: CARDIOLIPIN(Non-covalent)
CDL.7: 14 residues within 4Å:- Chain C: A.30, G.232, L.235, M.236
- Chain D: Y.220, K.223, R.224
- Chain F: H.72, R.73
- Chain G: I.29, A.33, L.34, R.40
- Ligands: CDL.19
11 PLIP interactions:5 interactions with chain D, 3 interactions with chain C, 2 interactions with chain G, 1 interactions with chain F- Hydrophobic interactions: D:Y.220, D:Y.220, C:A.30, C:L.235, C:M.236, G:I.29
- Hydrogen bonds: D:R.224, G:R.40
- Salt bridges: D:K.223, D:R.224, F:R.73
CDL.19: 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.7, PEE.8
6 PLIP interactions:2 interactions with chain C, 1 interactions with chain F, 3 interactions with chain G- Hydrophobic interactions: C:W.31
- Hydrogen bonds: C:A.30
- Salt bridges: F:H.72, G:R.40, G:R.40, G:R.40
CDL.26: 15 residues within 4Å:- Chain M: A.30, F.90, 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, L.34, R.40
- Ligands: CDL.38
15 PLIP interactions:5 interactions with chain M, 6 interactions with chain N, 3 interactions with chain Q, 1 interactions with chain P- Hydrophobic interactions: M:A.30, M:F.90, M:L.235, M:L.235, M:M.236, N:Y.220, N:Y.220, Q:I.29
- Hydrogen bonds: N:Y.220, N:R.224, Q:R.40
- Salt bridges: N:K.223, N:R.224, Q:R.40, P:R.73
CDL.38: 13 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, V.45, V.48
- Ligands: CDL.26, PEE.27
10 PLIP interactions:1 interactions with chain P, 4 interactions with chain M, 5 interactions with chain Q- Salt bridges: P:H.72, Q:R.40, Q:R.40, Q:R.40
- Hydrophobic interactions: M:W.31, Q:V.37, Q:V.48
- Hydrogen bonds: M:A.30, M:W.31, M:Y.105
- 2 x GOL: GLYCEROL(Non-functional Binders)
GOL.13: 7 residues within 4Å:- Chain C: F.64, V.67, A.68, R.81, N.256, F.257
- Chain D: Y.115
4 PLIP interactions:3 interactions with chain C, 1 interactions with chain D- Hydrogen bonds: C:F.64, C:R.81, C:N.256, D:Y.115
GOL.32: 6 residues within 4Å:- Chain M: F.64, 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:N.256, N:Y.115
- 2 x HEC: HEME C(Covalent)
HEC.14: 18 residues within 4Å:- Chain D: V.32, V.36, C.37, C.40, H.41, N.105, A.108, P.110, P.111, R.120, Y.126, V.127, 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.108, D:V.127, D:L.131, D:I.158, D:M.160, D:P.163
- Hydrogen bonds: D:Y.126, D:G.159
- Salt bridges: D:R.120
- pi-Stacking: D:H.41, D:H.41
- Metal complexes: D:H.41
HEC.33: 19 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, R.120, Y.126, V.127, L.131, F.153, I.158, G.159, M.160, P.163
15 PLIP interactions:15 interactions with chain N,- Hydrophobic interactions: N:V.32, N:A.108, N:P.110, N:V.127, N:L.131, N:I.158, N:M.160, N:P.163
- Hydrogen bonds: N:Y.126, N:G.159
- Salt bridges: N:R.120
- pi-Stacking: N:H.41, N:H.41
- pi-Cation interactions: N:H.41
- Metal complexes: N:H.41
- 2 x BOG: octyl beta-D-glucopyranoside(Non-covalent)
BOG.15: 10 residues within 4Å:- Chain C: Y.76
- Chain D: Q.200, R.203, M.204, K.207, M.208
- Chain E: A.50, N.53, Q.57
- Chain J: D.37
7 PLIP interactions:1 interactions with chain C, 3 interactions with chain E, 2 interactions with chain D, 1 interactions with chain J- Hydrogen bonds: C:Y.76, E:N.53, D:Q.200, J:D.37
- Hydrophobic interactions: E:A.50, E:N.53
- Salt bridges: D:K.207
BOG.37: 9 residues within 4Å:- Chain M: Y.76
- Chain N: Q.200, R.203, M.204, K.207
- Chain O: A.50, N.53, Q.57
- Chain T: D.37
7 PLIP interactions:1 interactions with chain M, 3 interactions with chain O, 3 interactions with chain N- Hydrogen bonds: M:Y.76, O:N.53, N:Q.200, N:R.203
- Hydrophobic interactions: O:A.50, O:N.53
- Salt bridges: N:K.207
- 2 x FES: FE2/S2 (INORGANIC) CLUSTER(Non-covalent)
FES.16: 9 residues within 4Å:- Chain E: C.139, H.141, L.142, G.143, C.144, C.158, H.161, G.162, 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: 9 residues within 4Å:- Chain O: C.139, H.141, L.142, G.143, C.144, C.158, H.161, G.162, 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., Ascochlorin is a novel, specific inhibitor of the mitochondrial cytochrome bc(1) complex. Biochim.Biophys.Acta (2010)
- Release Date
- 2010-01-05
- 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 3.21 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)
- 12 x UNL: UNKNOWN LIGAND
- 4 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)
- 4 x 3H1: 3-chloro-4,6-dihydroxy-2-methyl-5-{(2E,4E)-3-methyl-5-[(1R,2R,6R)-1,2,6-trimethyl-3-oxocyclohexyl]penta-2,4-dien-1-yl}benzaldehyde(Non-covalent)
- 4 x CDL: CARDIOLIPIN(Non-covalent)
- 2 x GOL: GLYCEROL(Non-functional Binders)
- 2 x HEC: HEME C(Covalent)
- 2 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., Ascochlorin is a novel, specific inhibitor of the mitochondrial cytochrome bc(1) complex. Biochim.Biophys.Acta (2010)
- Release Date
- 2010-01-05
- 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.