- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.79 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)
- 11 x UNL: UNKNOWN LIGAND(Non-functional Binders)
UNL.2: 1 residues within 4Å:- Chain A: G.285
No protein-ligand interaction detected (PLIP)UNL.10: 1 residues within 4Å:- Ligands: PEE.8
No protein-ligand interaction detected (PLIP)UNL.11: 3 residues within 4Å:- Chain C: R.81, N.82, A.85
2 PLIP interactions:2 interactions with chain C- Hydrogen bonds: C:R.81, C:N.82
UNL.12: 3 residues within 4Å:- Chain C: Y.108, L.308, F.367
2 PLIP interactions:2 interactions with chain C- Hydrogen bonds: C:Y.108, C:Y.108
UNL.18: 3 residues within 4Å:- Chain C: L.79
- Chain D: M.204
- Chain E: Q.57
1 PLIP interactions:1 interactions with chain E- Hydrogen bonds: E:Q.57
UNL.30: 3 residues within 4Å:- Chain M: L.241
- Ligands: UNL.31, UNL.40
No protein-ligand interaction detected (PLIP)UNL.31: 1 residues within 4Å:- Ligands: UNL.30
No protein-ligand interaction detected (PLIP)UNL.32: 1 residues within 4Å:- Ligands: PEE.28
No protein-ligand interaction detected (PLIP)UNL.33: 3 residues within 4Å:- Chain M: L.251, G.252, E.272
2 PLIP interactions:2 interactions with chain M- Hydrogen bonds: M:E.272
- Water bridges: M:E.272
UNL.34: 3 residues within 4Å:- Chain M: Y.108, L.308, H.309
2 PLIP interactions:2 interactions with chain M- Hydrogen bonds: M:Y.108, M:H.309
UNL.40: 4 residues within 4Å:- Chain N: M.204
- Chain O: Q.57
- Ligands: UNL.30, BOG.37
1 PLIP interactions:1 interactions with chain O- Hydrogen bonds: O:Q.57
- 4 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)
HEM.3: 21 residues within 4Å:- Chain C: Q.45, I.46, G.49, L.50, L.52, A.53, R.81, H.84, F.91, L.124, T.127, A.128, G.131, Y.132, L.134, P.135, F.180, H.183, F.184, P.187, I.190
18 PLIP interactions:18 interactions with chain C,- Hydrophobic interactions: C:Q.45, C:I.46, C:L.50, C:L.52, C:F.91, C:T.127, C:L.134, C:F.180, C:F.184, C:I.190
- Salt bridges: C:R.81, C:R.81
- pi-Stacking: C:H.84, C:H.84, C:H.183, C:H.183
- Metal complexes: C:H.84, C:H.183
HEM.4: 23 residues within 4Å:- Chain C: W.32, G.35, 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, I.190, T.194, H.197, L.198, L.201, S.206, N.207
- Ligands: UQ.6
23 PLIP interactions:23 interactions with chain C,- Hydrophobic interactions: C:L.38, C:L.38, C:F.91, C:I.95, C:I.99, C:T.113, C:V.118, C:L.120, C:L.120, C:L.120, C:I.190, 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
- Salt bridges: C:H.98, C:R.101, C:R.101
- Metal complexes: C:H.98, C:H.197
HEM.22: 23 residues within 4Å:- Chain M: Q.45, I.46, G.49, L.50, L.52, A.53, V.67, R.81, H.84, A.85, A.88, F.91, L.124, T.127, A.128, G.131, Y.132, L.134, P.135, H.183, F.184, P.187, I.190
18 PLIP interactions:18 interactions with chain M,- Hydrophobic interactions: M:Q.45, M:I.46, M:L.50, M:L.52, M:V.67, M:A.85, M:A.88, M:F.91, M:T.127, M:L.134, M:F.184, M:I.190
- Salt bridges: M:R.81, M:R.81
- pi-Stacking: M:H.84, M:H.183
- Metal complexes: M:H.84, M:H.183
HEM.23: 24 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, I.190, T.194, H.197, L.198, L.201, S.206, N.207
- Ligands: UQ.26
24 PLIP interactions:24 interactions with chain M,- Hydrophobic interactions: M:L.38, M:L.38, M:F.91, M:I.95, M:I.99, M:T.113, M:V.118, M:L.120, M:L.120, M:L.120, M:I.190, M:L.198, M:L.201, M:L.201
- Hydrogen bonds: M:G.35, M:S.206, M:N.207
- Water bridges: M:F.34, M:S.36
- Salt bridges: M:H.98, M:R.101, M:R.101
- Metal complexes: M:H.98, M:H.197
- 2 x FNM: (5S)-5-methyl-2-(methylsulfanyl)-5-phenyl-3-(phenylamino)-3,5-dihydro-4H-imidazol-4-one(Non-covalent)
FNM.5: 16 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, Y.279
11 PLIP interactions:11 interactions with chain C- Hydrophobic interactions: C:F.129, C:F.129, C:Y.132, C:I.147, C:I.147, C:I.269, C:P.271, C:E.272, C:Y.279
- Hydrogen bonds: C:E.272
- pi-Stacking: C:F.275
FNM.25: 15 residues within 4Å:- Chain M: 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
11 PLIP interactions:11 interactions with chain M- Hydrophobic interactions: M:A.128, M:F.129, M:F.129, M:Y.132, M:I.147, M:I.147, M:I.269, M:P.271, M:E.272
- 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.6: 13 residues within 4Å:- Chain C: S.18, L.22, I.28, A.39, L.198, L.201, H.202, S.206, F.221, Y.225, D.229
- Ligands: HEM.4, BOG.13
3 PLIP interactions:3 interactions with chain C- Hydrophobic interactions: C:A.39, C:F.221
- Hydrogen bonds: C:S.206
UQ.26: 13 residues within 4Å:- Chain M: S.18, L.19, L.22, A.24, I.28, A.39, L.198, L.201, H.202, S.206, F.221, D.229
- Ligands: HEM.23
4 PLIP interactions:4 interactions with chain M- Hydrophobic interactions: M:A.39, M:L.198, M:F.221
- Hydrogen bonds: M:S.206
- 2 x AZI: AZIDE ION(Non-covalent)
AZI.9: 2 residues within 4Å:- Chain C: R.81, N.256
2 PLIP interactions:2 interactions with chain C- Hydrogen bonds: C:R.81, C:R.81
AZI.29: 3 residues within 4Å:- Chain M: R.81, N.256
- Chain N: Y.115
4 PLIP interactions:1 interactions with chain N, 3 interactions with chain M- Hydrogen bonds: N:Y.115, M:R.81, M:R.81, M:N.256
- 6 x BOG: octyl beta-D-glucopyranoside(Non-covalent)
BOG.13: 7 residues within 4Å:- Chain C: S.18, L.19, I.195, L.198, T.199, H.202
- Ligands: UQ.6
4 PLIP interactions:4 interactions with chain C- Hydrophobic interactions: C:L.19, C:I.195, C:L.198
- Salt bridges: C:H.202
BOG.16: 12 residues within 4Å:- Chain C: Y.76
- Chain D: Q.200, R.203, M.204, K.207, I.211
- Chain E: Y.49, A.50, N.53, Q.57
- Chain J: D.37
- Ligands: BOG.17
9 PLIP interactions:3 interactions with chain D, 3 interactions with chain E, 1 interactions with chain J, 2 interactions with chain C- Hydrophobic interactions: D:I.211, E:Y.49, E:A.50
- Hydrogen bonds: D:Q.200, E:N.53, J:D.37, C:Y.76, C:Y.76
- Salt bridges: D:K.207
BOG.17: 10 residues within 4Å:- Chain C: Y.76
- Chain D: L.21, H.23, V.54, W.192, P.196, D.199, Q.200, R.203
- Ligands: BOG.16
6 PLIP interactions:5 interactions with chain D, 1 interactions with chain C- Hydrophobic interactions: D:L.21, D:V.54
- Hydrogen bonds: D:Q.200, D:R.203, C:Y.76
- Salt bridges: D:R.203
BOG.24: 7 residues within 4Å:- Chain M: K.13, M.14, I.15, N.17, S.18, T.199, H.202
3 PLIP interactions:3 interactions with chain M- Hydrophobic interactions: M:I.15
- Hydrogen bonds: M:M.14, M:N.17
BOG.37: 13 residues within 4Å:- Chain M: Y.76, L.241
- Chain N: Q.200, R.203, M.204, K.207, I.211
- Chain O: Y.49, A.50, N.53, Q.57
- Ligands: BOG.38, UNL.40
9 PLIP interactions:2 interactions with chain M, 3 interactions with chain N, 1 interactions with chain T, 3 interactions with chain O- Hydrophobic interactions: M:L.241, N:I.211, O:Y.49, O:A.50
- Hydrogen bonds: M:Y.76, N:Q.200, T:D.37, O:N.53
- Salt bridges: N:K.207
BOG.38: 2 residues within 4Å:- Chain N: Q.200
- Ligands: BOG.37
1 PLIP interactions:1 interactions with chain N- Hydrogen bonds: N:Q.200
- 2 x HEC: HEME C(Covalent)
HEC.14: 19 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, F.153, I.158, G.159, M.160, P.163, I.164
12 PLIP interactions:12 interactions with chain D,- Hydrophobic interactions: D:V.32, D:A.108, D:P.110, D:I.116, 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
- Metal complexes: D:H.41
HEC.35: 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, I.116, R.120, Y.126, F.153, I.158, G.159, M.160, P.163, I.164
14 PLIP interactions:14 interactions with chain N,- Hydrophobic interactions: N:V.32, N:A.108, N:P.110, N:I.116, 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-Cation interactions: N:H.41, N:H.41
- Metal complexes: N:H.41
- 4 x CDL: CARDIOLIPIN(Non-covalent)
CDL.15: 14 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: I.29, A.33, R.40
- Ligands: CDL.20
10 PLIP interactions:2 interactions with chain C, 5 interactions with chain D, 2 interactions with chain G, 1 interactions with chain F- Hydrophobic interactions: C:A.30, D:Y.220
- Hydrogen bonds: C:N.33, D:R.224, G:R.40, G:R.40
- Salt bridges: D:K.223, D:R.224, D:K.231, F:R.73
CDL.20: 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: PEE.8, CDL.15
9 PLIP interactions:1 interactions with chain F, 3 interactions with chain C, 5 interactions with chain G- Salt bridges: F:H.72, G:R.40, G:R.40, G:R.40
- Hydrophobic interactions: C:W.31, G:F.41, G:F.41
- Hydrogen bonds: C:A.30, C:W.31
CDL.36: 15 residues within 4Å:- Chain M: A.30, N.33, G.232, L.235
- Chain N: Y.220, K.223, R.224, K.231
- Chain P: H.72, R.73
- Chain Q: I.26, I.29, A.33, R.40
- Ligands: CDL.41
16 PLIP interactions:3 interactions with chain M, 8 interactions with chain N, 4 interactions with chain Q, 1 interactions with chain P- Hydrophobic interactions: M:A.30, M:L.235, N:Y.220, N:Y.220, N:Y.220, Q:I.26, Q:I.29
- Hydrogen bonds: M:N.33, N:Y.220, N:R.224, Q:R.40, Q:R.40
- Salt bridges: N:K.223, N:R.224, N:K.231, P:R.73
CDL.41: 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.28, CDL.36
11 PLIP interactions:6 interactions with chain Q, 1 interactions with chain P, 4 interactions with chain M- Hydrophobic interactions: Q:F.41, Q:F.41, Q:Q.44, M:W.31
- Salt bridges: Q:R.40, Q:R.40, Q:R.40, P:H.72
- Hydrogen bonds: M:A.30, M:W.31, M:Y.105
- 2 x FES: FE2/S2 (INORGANIC) CLUSTER(Non-covalent)
FES.19: 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
4 PLIP interactions:4 interactions with chain E,- Metal complexes: E:C.139, E:H.141, E:C.158, E:H.161
FES.39: 9 residues within 4Å:- Chain O: C.139, H.141, L.142, C.144, C.158, C.160, 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
- Huang, L. et al., FAMOXADONE AND RELATED INHIBITORS BIND LIKE METHOXY ACRYLATE INHIBITORS IN THE Qo SITE OF THE BC1 COMPL AND FIX THE RIESKE IRON-SULFUR PROTEIN IN A POSITIO CLOSE TO BUT DISTINCT FROM THAT SEEN WITH STIGMATELLIN AND OTHER "DISTAL" Qo INHIBITORS. To be Published
- Release Date
- 2010-02-02
- 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 5, RIESKE IRONSULFUR PROTEIN, 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 2.79 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)
- 11 x UNL: UNKNOWN LIGAND(Non-functional Binders)
- 4 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)
- 2 x FNM: (5S)-5-methyl-2-(methylsulfanyl)-5-phenyl-3-(phenylamino)-3,5-dihydro-4H-imidazol-4-one(Non-covalent)
- 2 x UQ: Coenzyme Q10, (2Z,6E,10Z,14E,18E,22E,26Z)-isomer(Non-covalent)
- 2 x AZI: AZIDE ION(Non-covalent)
- 6 x BOG: octyl beta-D-glucopyranoside(Non-covalent)
- 2 x HEC: HEME C(Covalent)
- 4 x CDL: CARDIOLIPIN(Non-covalent)
- 2 x FES: FE2/S2 (INORGANIC) CLUSTER(Non-covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Huang, L. et al., FAMOXADONE AND RELATED INHIBITORS BIND LIKE METHOXY ACRYLATE INHIBITORS IN THE Qo SITE OF THE BC1 COMPL AND FIX THE RIESKE IRON-SULFUR PROTEIN IN A POSITIO CLOSE TO BUT DISTINCT FROM THAT SEEN WITH STIGMATELLIN AND OTHER "DISTAL" Qo INHIBITORS. To be Published
- Release Date
- 2010-02-02
- 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 5, RIESKE IRONSULFUR PROTEIN, 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.