- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 3.51 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)
- 6 x BOG: octyl beta-D-glucopyranoside(Non-covalent)
BOG.2: 6 residues within 4Å:- Chain C: M.14, S.18, L.198, T.199, H.202
- Ligands: UQ.7
5 PLIP interactions:5 interactions with chain C- Hydrophobic interactions: C:L.198
- Hydrogen bonds: C:S.18, C:T.199, C:T.199
- Salt bridges: C:H.202
BOG.10: 8 residues within 4Å:- Chain C: Y.76
- Chain D: H.23, V.54, P.196, D.199, Q.200, R.203
- Ligands: BOG.13
6 PLIP interactions:5 interactions with chain D, 1 interactions with chain C- Hydrophobic interactions: D:V.54, D:D.199
- Hydrogen bonds: D:Q.200, D:R.203, C:Y.76
- Salt bridges: D:R.203
BOG.13: 10 residues within 4Å:- Chain C: Y.76
- Chain D: Q.200, R.203, M.204, K.207
- Chain E: A.50, N.53, Q.57
- Chain J: D.37
- Ligands: BOG.10
6 PLIP interactions:2 interactions with chain D, 2 interactions with chain E, 1 interactions with chain J, 1 interactions with chain C- Hydrogen bonds: D:Q.200, E:N.53, J:D.37, C:Y.76
- Salt bridges: D:K.207
- Hydrophobic interactions: E:A.50
BOG.17: 8 residues within 4Å:- Chain M: M.14, I.15, N.17, S.18, L.19, L.198, T.199, H.202
5 PLIP interactions:5 interactions with chain M- Hydrophobic interactions: M:I.15, M:L.19, M:L.198
- Hydrogen bonds: M:N.17, M:S.18
BOG.29: 11 residues within 4Å:- Chain M: Y.76, L.241
- Chain N: Q.200, R.203, M.204, K.207, I.211
- Chain O: A.50, N.53, Q.57
- Ligands: BOG.30
6 PLIP interactions:3 interactions with chain N, 1 interactions with chain M, 2 interactions with chain O- Hydrophobic interactions: N:I.211, M:L.241, O:A.50
- Hydrogen bonds: N:Q.200, O:N.53
- Salt bridges: N:K.207
BOG.30: 2 residues within 4Å:- Chain N: Q.200
- Ligands: BOG.29
2 PLIP interactions:2 interactions with chain N- Hydrogen bonds: N:Q.200, N:Q.200
- 2 x AZI: AZIDE ION(Non-covalent)
- 4 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)
HEM.4: 21 residues within 4Å:- Chain C: Q.45, I.46, G.49, L.50, L.52, A.53, Y.56, 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, Y.274
15 PLIP interactions:15 interactions with chain C,- Hydrophobic interactions: C:Q.45, C:I.46, C:L.52, C:L.52, C:A.53, C:Y.56, C:L.124, C:T.127, C:L.134, C:F.184, C:P.187
- Salt bridges: C:R.81, C:R.81
- Metal complexes: C:H.84, C:H.183
HEM.5: 24 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, I.190, T.194, H.197, L.198, L.201, S.206, N.207
- Ligands: UQ.7
23 PLIP interactions:23 interactions with chain C,- Hydrophobic interactions: 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.121, C:I.190, C:L.198, C:L.201, C:L.201
- Hydrogen bonds: C:G.35, C:N.207
- Water bridges: C:W.32, C:R.101, C:S.206
- Salt bridges: C:H.98, C:R.101, C:R.101
- Metal complexes: C:H.98, C:H.197
HEM.19: 21 residues within 4Å:- Chain M: Q.45, I.46, G.49, L.50, L.52, A.53, Y.56, 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, Y.274
15 PLIP interactions:15 interactions with chain M,- Hydrophobic interactions: M:Q.45, M:I.46, M:L.52, M:L.52, M:A.53, M:Y.56, M:L.124, M:T.127, M:L.134, M:F.184, M:P.187
- Salt bridges: M:R.81, M:R.81
- Metal complexes: M:H.84, M:H.183
HEM.20: 24 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, I.190, T.194, H.197, L.198, L.201, S.206, N.207
- Ligands: UQ.22
26 PLIP interactions:26 interactions with chain M,- Hydrophobic interactions: 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:I.190, M:L.198, M:L.201, M:L.201
- Hydrogen bonds: M:G.35, M:N.207
- Water bridges: M:W.32, M:S.36, M:R.101, M:S.206
- Salt bridges: M:H.98, M:R.101, M:R.101
- pi-Stacking: M:H.98, M:H.98
- Metal complexes: M:H.98, M:H.197
- 2 x ICX: methyl N-[(5Z)-6-({[4-(4-iodobenzyl)phenyl]carbonyl}amino)hex-5-enoyl]glycinate(Non-covalent)
ICX.6: 15 residues within 4Å:- Chain C: A.126, Y.132, W.142, G.143, V.146, I.147, I.269, P.271, E.272, Y.274, F.275, A.278, Y.279, L.282
- Chain O: H.161
11 PLIP interactions:11 interactions with chain C- Hydrophobic interactions: C:V.146, C:I.147, C:I.147, C:I.269, C:I.269, C:F.275, C:F.275, C:A.278, C:L.282
- Hydrogen bonds: C:E.272
- pi-Stacking: C:F.275
ICX.21: 18 residues within 4Å:- Chain E: H.161
- Chain M: A.128, F.129, Y.132, W.142, G.143, V.146, I.147, I.269, K.270, P.271, E.272, Y.274, F.275, A.278, Y.279, L.282, L.295
11 PLIP interactions:11 interactions with chain M- Hydrophobic interactions: M:V.146, M:I.147, M:I.147, M:I.269, M:I.269, M:F.275, M:A.278, M:L.282, 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: 13 residues within 4Å:- Chain C: S.18, L.22, P.23, I.28, S.36, A.39, L.198, H.202, S.206, F.221, D.229
- Ligands: BOG.2, HEM.5
4 PLIP interactions:4 interactions with chain C- Hydrophobic interactions: C:A.39, C:L.198, C:F.221
- Hydrogen bonds: C:S.206
UQ.22: 11 residues within 4Å:- Chain M: S.18, L.19, L.22, I.28, L.198, H.202, S.206, F.221, Y.225, D.229
- Ligands: HEM.20
5 PLIP interactions:5 interactions with chain M- Hydrophobic interactions: M:L.19, M:L.198, M:F.221
- Hydrogen bonds: M:S.206
- Water bridges: M:S.36
- 2 x HEC: HEME C(Covalent)
HEC.11: 21 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, L.130, L.131, F.153, I.158, G.159, M.160, P.163, V.186
15 PLIP interactions:15 interactions with chain D,- Hydrophobic interactions: D:V.32, D:A.108, D:P.110, D:I.116, D:L.130, D:L.131, D:I.158, D:M.160, D:P.163, D:V.186
- Hydrogen bonds: D:G.159
- Salt bridges: D:R.120
- pi-Stacking: D:H.41, D:H.41
- 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, L.109, P.110, P.111, L.113, R.120, Y.126, L.130, L.131, F.153, I.158, G.159, M.160, P.163, V.186
14 PLIP interactions:14 interactions with chain N,- Hydrophobic interactions: N:V.32, N:A.108, N:L.113, N:L.130, N:L.131, N:I.158, N:M.160, N:P.163, N:V.186
- Hydrogen bonds: N:G.159
- Salt bridges: N:R.120
- pi-Stacking: N:H.41
- pi-Cation interactions: N:H.41
- Metal complexes: N:H.41
- 4 x CDL: CARDIOLIPIN(Non-covalent)
CDL.12: 15 residues within 4Å:- Chain C: A.30, N.33, K.228, L.231, G.232, L.235
- Chain D: Y.220, K.223, R.224
- Chain F: H.72, R.73
- Chain G: A.33, V.37, R.40
- Ligands: CDL.16
8 PLIP interactions:1 interactions with chain G, 3 interactions with chain C, 3 interactions with chain D, 1 interactions with chain F- Hydrogen bonds: G:R.40, C:N.33
- Hydrophobic interactions: C:A.30
- Salt bridges: C:K.228, D:K.223, D:R.224, D:K.231, F:R.73
CDL.16: 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.9, CDL.12
7 PLIP interactions:3 interactions with chain G, 3 interactions with chain C, 1 interactions with chain F- Hydrogen bonds: G:R.40, C:A.30, C:Y.105
- Salt bridges: G:R.40, G:R.40, F:H.72
- Hydrophobic interactions: C:W.31
CDL.23: 15 residues within 4Å:- Chain M: A.30, N.33, K.228, L.231, G.232, L.235
- Chain N: Y.220, K.223, R.224, K.231
- Chain P: H.72, R.73
- Chain Q: L.34, R.40
- Ligands: CDL.24
8 PLIP interactions:3 interactions with chain N, 1 interactions with chain P, 2 interactions with chain M, 2 interactions with chain Q- Salt bridges: N:K.223, N:R.224, N:K.231, P:R.73, M:K.228, Q:R.40
- Hydrophobic interactions: M:A.30
- Hydrogen bonds: Q:R.40
CDL.24: 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: CDL.23, PEE.25
8 PLIP interactions:3 interactions with chain M, 4 interactions with chain Q, 1 interactions with chain P- Hydrophobic interactions: M:W.31, Q:V.37
- Hydrogen bonds: M:A.30, M:Y.105, Q:R.40
- Salt bridges: Q:R.40, Q:R.40, P:H.72
- 2 x FES: FE2/S2 (INORGANIC) CLUSTER(Non-covalent)
FES.14: 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.33: 10 residues within 4Å:- Chain O: 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 O,- Metal complexes: O:C.139, O:H.141, O:C.158, O:H.161
- 4 x UNL: UNKNOWN LIGAND(Non-covalent)(Non-functional Binders)
UNL.15: 3 residues within 4Å:- Chain D: M.204
- Chain E: V.54, Q.57
2 PLIP interactions:2 interactions with chain E- Hydrogen bonds: E:Q.57, E:Q.57
UNL.27: 4 residues within 4Å:- Chain M: L.241
- Chain O: V.54
- Ligands: UNL.28, UNL.32
No protein-ligand interaction detected (PLIP)UNL.28: 1 residues within 4Å:- Ligands: UNL.27
No protein-ligand interaction detected (PLIP)UNL.32: 3 residues within 4Å:- Chain N: M.204
- Chain O: Q.57
- Ligands: UNL.27
1 PLIP interactions:1 interactions with chain O- Hydrogen bonds: O:Q.57
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Crowley, P.J. et al., The role of molecular modeling in the design of analogues of the fungicidal natural products crocacins A and D. Bioorg.Med.Chem. (2008)
- Release Date
- 2008-08-12
- 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
MITOCHONDRIAL UBIQUINOL-CYTOCHROME C REDUCTASE IRON-SULFUR PROTEIN: 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
MITOCHONDRIAL UBIQUINOL-CYTOCHROME C REDUCTASE IRON-SULFUR SUBUNIT, leader sequence: 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 3.51 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)
- 6 x BOG: octyl beta-D-glucopyranoside(Non-covalent)
- 2 x AZI: AZIDE ION(Non-covalent)
- 4 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)
- 2 x ICX: methyl N-[(5Z)-6-({[4-(4-iodobenzyl)phenyl]carbonyl}amino)hex-5-enoyl]glycinate(Non-covalent)
- 2 x UQ: Coenzyme Q10, (2Z,6E,10Z,14E,18E,22E,26Z)-isomer(Non-covalent)
- 2 x HEC: HEME C(Covalent)
- 4 x CDL: CARDIOLIPIN(Non-covalent)
- 2 x FES: FE2/S2 (INORGANIC) CLUSTER(Non-covalent)
- 4 x UNL: UNKNOWN LIGAND(Non-covalent)(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Crowley, P.J. et al., The role of molecular modeling in the design of analogues of the fungicidal natural products crocacins A and D. Bioorg.Med.Chem. (2008)
- Release Date
- 2008-08-12
- 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
MITOCHONDRIAL UBIQUINOL-CYTOCHROME C REDUCTASE IRON-SULFUR PROTEIN: 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
MITOCHONDRIAL UBIQUINOL-CYTOCHROME C REDUCTASE IRON-SULFUR SUBUNIT, leader sequence: 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.