MolNFT v1 · #18444 · protein
Bovine cytochrome BC1 complex with stigmatellin bound
1PP9 · Ubiquinol-cytochrome C reductase complex core protein I…: “Bovine cytochrome BC1 complex with stigmatellin bound”. X-ray diffraction, 10 ligands (PEE, JZR, HEM), 20 pockets (best druggability 0.85). MolNFT v1 #18444 on GenesisL1: 3D…
- PDB
- 1PP9
- Type
- protein
- Length
- 4,025 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
- PEE, JZR, HEM, CDL, SMA, UQ, HEC, FES, AZI, PO4
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 13 distinct chains · 53% helix, 12% 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 | 442 | 47% helix, 19% strand | P31800 |
| B | Ubiquinol-cytochrome C reductase complex core protein 2, mitochondrial (EC 1.10.2.2) | protein | 423 | 47% helix, 20% strand | P23004 |
| C | Cytochrome B (EC 1.10.2.2) | protein | 365 | 72% 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 | 32% 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 | 55% 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 | 42 | 10% helix, 19% strand | P13272 |
| J, W | Ubiquinol-cytochrome C reductase complex 7.2 kda protein (EC 1.10.2.2) | protein | 62 | 76% helix, 0% strand | P00130 |
| O | Ubiquinol-cytochrome C reductase complex core protein 2, mitochondrial (EC 1.10.2.2) | protein | 424 | 47% helix, 20% strand | P23004 |
| P | Cytochrome B (EC 1.10.2.2) | protein | 370 | 70% helix, 2% strand | P00157 |
| T | Ubiquinol-cytochrome C reductase complex ubiquinone-binding protein qp-C (EC 1.10.2.2) | protein | 74 | 55% helix, 12% strand | P13271 |
Ligands and binding sites
- PEE · 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine · ligand · 9 copies · chains A, C, F, G, D, E, J, N, P, Q, S, T, R, W
- JZR · hexyl beta-D-glucopyranoside · ligand · 6 copies · chains A, C, D, F, N, O, P, Q, B, S
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains C, P
- 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
- UQ · Coenzyme Q10, (2Z,6E,10Z,14E,18E,22E,26Z)-isomer · 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
- AZI · Azide ion · ion · 4 copies · chains A, C, D, E, G, P, Q
- PO4 · Phosphate ion · ion · 2 copies · chains B, S, F, O
- GOL · Glycerol · additive · 4 copies · chains B, I, C, 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 | 462 | 0.85 | 0.92 | 48 | HEM, GOL |
| 2 | 721 | 0.83 | 0.86 | 70 | empty |
| 3 | 764 | 0.82 | 0.85 | 71 | HEM, GOL |
| 4 | 721 | 0.82 | 0.85 | 65 | PEE |
| 5 | 741 | 0.81 | 0.85 | 70 | empty |
Interfaces
52 interfaces between chains.
- A–B · 2398 Ų buried · 42 hydrogen bonds · protein-protein
- N–O · 2368 Ų buried · 46 hydrogen bonds · protein-protein
- P–Q · 1721 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 1715 Ų buried · 16 hydrogen bonds · protein-protein
- B–I · 1690 Ų buried · 29 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 4 cofactor (disulfide, heme c attachment).
Compared structures
- 1PP9 · Bovine cytochrome bc1 complex with stigmatellin bound · the same entry in another collection · chain N against N, 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 1PP9 · PDBe 1PP9 · UniProt P31800 · UniProt P23004 · UniProt P00157 · UniProt P00125 · UniProt P13272 · UniProt P00129 · UniProt P13271 · UniProt P00126 · UniProt P00130
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