- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 3.06 Å
- Oligo State
- hetero-2-2-2-2-2-2-2-2-2-2-mer
- Ligands
- 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)
IKR.3: 18 residues within 4Å:- Chain C: M.125, 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, A.278, Y.279
12 PLIP interactions:12 interactions with chain C- Hydrophobic interactions: C:F.129, C:F.129, C:Y.132, C:I.147, C:I.269, C:P.271, C:F.275, C:F.275, C:A.278, C:Y.279
- Hydrogen bonds: C:E.272
- pi-Stacking: C:F.275
IKR.18: 18 residues within 4Å:- Chain M: M.125, 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, A.278, Y.279
11 PLIP interactions:11 interactions with chain M- Hydrophobic interactions: M:F.129, M:F.129, M:Y.132, M:I.269, M:P.271, M:F.275, M:F.275, M:A.278, M:Y.279
- 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.4: 14 residues within 4Å:- Chain C: S.18, L.19, L.22, I.28, S.36, A.39, M.43, L.198, L.201, H.202, S.206, F.221, D.229
- Ligands: HEM.2
6 PLIP interactions:6 interactions with chain C- Hydrophobic interactions: C:L.19, C:A.39, C:L.198
- Hydrogen bonds: C:S.206
- Water bridges: C:S.36
- pi-Stacking: C:F.221
UQ.19: 16 residues within 4Å:- Chain M: S.18, L.19, L.22, A.24, I.28, S.36, A.39, M.43, L.198, L.201, H.202, S.206, F.221, Y.225, D.229
- Ligands: HEM.16
5 PLIP interactions:5 interactions with chain M- Hydrophobic interactions: M:L.19, M:A.39, M:L.198, M:F.221
- Hydrogen bonds: M:S.206
- 4 x CDL: CARDIOLIPIN(Non-covalent)
CDL.5: 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.10
9 PLIP interactions:3 interactions with chain C, 5 interactions with chain G, 1 interactions with chain F- Hydrophobic interactions: C:W.31, G:V.37, G:F.41
- Hydrogen bonds: C:A.30, C:Y.105
- Salt bridges: G:R.40, G:R.40, G:R.40, F:H.72
CDL.10: 13 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: L.34, R.40
- Ligands: CDL.5
10 PLIP interactions:5 interactions with chain D, 3 interactions with chain C, 1 interactions with chain G, 1 interactions with chain F- Hydrophobic interactions: D:Y.220, D:Y.220, C:A.30
- Salt bridges: D:K.223, D:R.224, D:K.231, C:K.228, F:R.73
- Hydrogen bonds: C:N.33, G:R.40
CDL.20: 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.21, CDL.25
10 PLIP interactions:6 interactions with chain Q, 3 interactions with chain M, 1 interactions with chain P- Hydrophobic interactions: Q:V.37, 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:Y.105
CDL.25: 13 residues within 4Å:- Chain M: A.30, N.33, K.228, G.232, L.235
- Chain N: Y.220, K.223, R.224
- Chain P: H.72, R.73
- Chain Q: L.34, R.40
- Ligands: CDL.20
12 PLIP interactions:6 interactions with chain N, 3 interactions with chain M, 1 interactions with chain P, 2 interactions with chain Q- Hydrophobic interactions: N:Y.220, N:Y.220, M:A.30
- 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, P:R.73, Q:R.40
- 6 x PEE: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine(Non-covalent)
PEE.6: 19 residues within 4Å:- Chain C: W.31, F.96, L.97, I.99, Y.104, Y.105, F.277, T.317, F.326, W.327, L.333, L.334, T.337, Y.359
- Chain F: Y.29
- Chain G: Q.44, V.48, F.52
- Ligands: CDL.5
18 PLIP interactions:17 interactions with chain C, 1 interactions with chain G- Hydrophobic interactions: 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.277, C:F.326, C:F.326, C:W.327, C:W.327, C:L.334, G:F.52
- Hydrogen bonds: C:Y.104, C:Y.104, C:Y.105
PEE.7: 4 residues within 4Å:- Chain A: Y.442
- Chain C: H.222, I.230
- Ligands: PEE.14
3 PLIP interactions:3 interactions with chain C- Hydrophobic interactions: C:I.230
- Salt bridges: C:H.222, C:H.222
PEE.14: 15 residues within 4Å:- Chain A: Y.442
- Chain C: F.227, I.230
- Chain D: M.222, K.226
- Chain E: Y.37, T.40, T.47, A.48, K.52
- Chain J: F.11, A.18, A.25, E.29
- Ligands: PEE.7
5 PLIP interactions:1 interactions with chain D, 2 interactions with chain J, 2 interactions with chain E- Salt bridges: D:K.226
- Hydrophobic interactions: J:A.25, E:T.47, E:A.48
- Hydrogen bonds: J:F.11
PEE.21: 18 residues within 4Å:- Chain M: W.31, F.96, L.97, I.99, Y.104, Y.105, F.277, T.317, F.326, W.327, L.333, T.337, Y.359
- Chain P: Y.29
- Chain Q: Q.44, V.48, F.52
- Ligands: CDL.20
17 PLIP interactions:1 interactions with chain Q, 16 interactions with chain M- Hydrophobic interactions: Q:F.52, M:W.31, M:W.31, M:F.96, M:F.96, M:L.97, M:I.99, M:Y.104, M:Y.105, M:F.277, M:F.277, M:F.326, M:F.326, M:W.327, M:W.327
- Hydrogen bonds: M:Y.104, M:Y.105
PEE.22: 4 residues within 4Å:- Chain K: S.439, Y.442
- Chain M: H.222
- Ligands: PEE.29
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.29: 21 residues within 4Å:- Chain K: Y.442
- Chain M: F.227, I.230, L.233, L.237
- Chain N: K.226
- Chain O: Y.37, T.40, C.44, T.47, A.48, A.51, K.52
- Chain T: F.11, T.14, A.18, V.21, V.22, A.25, E.29
- Ligands: PEE.22
9 PLIP interactions:2 interactions with chain M, 4 interactions with chain T, 2 interactions with chain O, 1 interactions with chain N- Hydrophobic interactions: M:L.233, M:L.237, T:V.21, T:V.22, T:A.25, O:T.47
- Hydrogen bonds: T:R.12, O:T.40
- Salt bridges: N:K.226
- 2 x GOL: GLYCEROL(Non-functional Binders)
GOL.8: 6 residues within 4Å:- Chain C: F.64, V.67, 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:R.81, C:R.81, C:N.256, D:Y.115
GOL.23: 7 residues within 4Å:- Chain M: F.64, V.67, A.68, 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.9: 21 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, I.116, R.120, Y.126, V.127, L.131, F.153, I.158, G.159, M.160, P.163, I.164
14 PLIP interactions:14 interactions with chain D,- Hydrophobic interactions: D:V.32, D:A.39, D:A.108, D:I.116, D:V.127, 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
- Metal complexes: D:H.41
HEC.24: 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, V.127, L.131, F.153, I.158, G.159, M.160, P.163
14 PLIP interactions:14 interactions with chain N,- Hydrophobic interactions: N:V.32, N:A.108, N:I.116, 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
- pi-Cation interactions: N:H.41
- Metal complexes: N:H.41
- 5 x BOG: octyl beta-D-glucopyranoside(Non-covalent)
BOG.11: 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.12
7 PLIP interactions:2 interactions with chain E, 4 interactions with chain D, 1 interactions with chain C- Hydrophobic interactions: E:Y.49, D:I.211
- Hydrogen bonds: E:N.53, D:Q.200, D:R.203, C:Y.76
- Salt bridges: D:K.207
BOG.12: 3 residues within 4Å:- Chain D: Q.200, R.203
- Ligands: BOG.11
No protein-ligand interaction detected (PLIP)BOG.17: 4 residues within 4Å:- Chain M: M.14, L.198, T.199, H.202
1 PLIP interactions:1 interactions with chain M- Salt bridges: M:H.202
BOG.26: 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
- Chain T: D.37
5 PLIP interactions:2 interactions with chain O, 3 interactions with chain N- Hydrophobic interactions: O:Y.49
- Hydrogen bonds: O:N.53, N:Q.200, N:R.203
- Salt bridges: N:K.207
BOG.27: 1 residues within 4Å:- Chain N: Q.200
1 PLIP interactions:1 interactions with chain N- Hydrogen bonds: N:Q.200
- 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.28: 9 residues within 4Å:- Chain O: C.139, H.141, L.142, C.144, C.158, H.161, G.162, S.163, P.175
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 3.06 Å
- Oligo State
- hetero-2-2-2-2-2-2-2-2-2-2-mer
- Ligands
- 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)
- 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
- 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.