Research workbench
Bovine cytochrome BC1 complex with stigmatellin and antimycin
Analyse Bovine cytochrome BC1 complex with stigmatellin and antimycin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1PPJ
- Type
- protein
- Length
- 3,989 residues
- Chains
- 20
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquinol-cytochrome C reductase complex core protein I, mitochondrial…
- EC
- 1.10.2.2
- UniProt
- P31800, P23004, P00157, P00125, P13272, P00129, P13271, P00126, P00130
- Ligands
- JZR, HEM, PEE, CDL, SMA, ANY, HEC, FES, PO4, AZI
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 13 distinct chains · 50% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, N | Ubiquinol-cytochrome C reductase complex core protein I, mitochondrial (EC 1.10.2.2) | protein | 441 | 47% helix, 19% strand | P31800 |
| B | Ubiquinol-cytochrome C reductase complex core protein 2, mitochondrial (EC 1.10.2.2) | protein | 424 | 46% helix, 20% strand | P23004 |
| C, P | Cytochrome B (EC 1.10.2.2) | protein | 365 | 71% helix, 2% strand | P00157 |
| D, Q | Cytochrome C1, heme protein, mitochondrial (EC 1.10.2.2) | protein | 241 | 39% helix, 8% strand | P00125 |
| E, R | Ubiquinol-cytochrome C reductase iron-sulfur subunit, mitochondrial (EC 1.10.2.2) | protein | 196 | 30% helix, 21% strand | P13272 |
| F, S | Ubiquinol-cytochrome C reductase complex 14 kda protein (EC 1.10.2.2) | protein | 99 | 73% helix, 0% strand | P00129 |
| G | Ubiquinol-cytochrome C reductase complex ubiquinone-binding protein qp-C (EC 1.10.2.2) | protein | 73 | 56% helix, 12% strand | P13271 |
| H, U | Ubiquinol-cytochrome C reductase complex 11 kda protein (EC 1.10.2.2) | protein | 66 | 74% helix, 0% strand | P00126 |
| I, V | Ubiquinol-cytochrome C reductase iron-sulfur subunit, mitochondrial (EC 1.10.2.2) | protein | 43 | 9% helix, 19% strand | P13272 |
| J | Ubiquinol-cytochrome C reductase complex 7.2 kda protein (EC 1.10.2.2) | protein | 32 | 69% helix, 0% strand | P00130 |
| O | Ubiquinol-cytochrome C reductase complex core protein 2, mitochondrial (EC 1.10.2.2) | protein | 423 | 45% helix, 20% strand | P23004 |
| T | Ubiquinol-cytochrome C reductase complex ubiquinone-binding protein qp-C (EC 1.10.2.2) | protein | 74 | 55% helix, 12% strand | P13271 |
| W | Ubiquinol-cytochrome C reductase complex 7.2 kda protein (EC 1.10.2.2) | protein | 61 | 77% helix, 0% strand | P00130 |
Ligands and binding sites
- JZR · hexyl beta-D-glucopyranoside · ligand · 9 copies · chains A, C, D, G, F, N, O, P, Q, R, B, S
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains C, P
- PEE · 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine · ligand · 4 copies · chains C, F, G, D, E, J, P, S, T, Q, R, W
- CDL · Cardiolipin · ligand · 4 copies · chains C, D, F, G, P, Q, S, T
- SMA · Stigmatellin A · ligand · 2 copies · chains C, R, E, P
- ANY · 2-methyl-butyric acid 3-(3-formylamino-2-hydroxy-benzoylamino)-8-heptyl-2,6-dimethyl-4,9-dioxo-[1,5]dioxonan-7-yl ester · ligand · 2 copies · chains C, P
- HEC · Heme C · ligand · 2 copies · chains D, Q
- FES · Fe2/s2 (inorganic) cluster · ligand · 2 copies · chains E, R
- PO4 · Phosphate ion · ion · 5 copies · chains A, C, E, F, O, N, P, Q, B, S
- AZI · Azide ion · ion · 5 copies · chains A, C, D, E, G, O, V, P, Q
- GOL · Glycerol · additive · 6 copies · chains B, I, C, R, O, V, P
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 900 | 0.86 | 0.88 | 113 | GOL |
| 2 | 719 | 0.85 | 0.88 | 72 | AZI, HEM, GOL |
| 3 | 613 | 0.84 | 0.88 | 67 | empty |
| 4 | 768 | 0.83 | 0.86 | 70 | HEM, GOL |
| 5 | 1130 | 0.82 | 0.83 | 107 | PEE, CDL |
Interfaces
51 interfaces between chains.
- A–B · 2329 Ų buried · 44 hydrogen bonds · protein-protein
- N–O · 2322 Ų buried · 42 hydrogen bonds · protein-protein
- C–D · 1724 Ų buried · 15 hydrogen bonds · protein-protein
- P–Q · 1710 Ų buried · 18 hydrogen bonds · protein-protein
- O–V · 1676 Ų buried · 30 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 4 cofactor (disulfide, heme c attachment).
Compared structures
- 1PPJ · Bovine cytochrome bc1 complex with stigmatellin and antimycin · the same entry in another collection · chain H against H, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P31800
- Every structure of UniProt P23004
- Every structure of UniProt P00157
- Every structure of UniProt P00125
- Every structure of UniProt P13272
- Every structure of UniProt P00129
- Every structure of UniProt P13271
- Every structure of UniProt P00126
- Every structure of UniProt P00130
- Elsewhere: RCSB PDB 1PPJ · PDBe 1PPJ · UniProt P31800 · UniProt P23004 · UniProt P00157 · UniProt P00125 · UniProt P13272 · UniProt P00129 · UniProt P13271 · UniProt P00126 · UniProt P00130
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