MolNFT v1 · #103318 · protein
Structural analysis of atovaquone-inhibited cytochrome BC1 complex reveals the molecular basis of antimalarial drug action
4PD4 · Cytochrome B-C1 complex subunit 1, mitochondrial: “Structural analysis of atovaquone-inhibited cytochrome BC1 complex reveals the molecular basis of…”. X-ray diffraction, 7 ligands (3PH, HEM, UMQ), 20 pockets (best druggability…
- PDB
- 4PD4
- Type
- protein
- Length
- 2,185 residues
- Chains
- 11
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome B-C1 complex subunit 1, mitochondrial; Cytochrome B-C1 complex subunit 2…
- EC
- 1.10.2.2
- UniProt
- P07256, P07257, P00163, P07143, P08067, P00127, P00128, P08525, P22289
- Ligands
- 3PH, HEM, UMQ, AOQ, 3PE, UQ6, FES
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 11 distinct chains · 42% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytochrome B-C1 complex subunit 1, mitochondrial | protein | 431 | 41% helix, 18% strand | P07256 |
| B | Cytochrome B-C1 complex subunit 2, mitochondrial | protein | 352 | 39% helix, 18% strand | P07257 |
| C | Cytochrome B | protein | 385 | 66% helix, 2% strand | P00163 |
| D | Cytochrome C1, heme protein, mitochondrial | protein | 248 | 38% helix, 4% strand | P07143 |
| E | Cytochrome B-C1 complex subunit rieske, mitochondrial (EC 1.10.2.2) | protein | 185 | 22% helix, 22% strand | P08067 |
| F | Cytochrome B-C1 complex subunit 6 | protein | 74 | 70% helix, 0% strand | P00127 |
| G | Cytochrome B-C1 complex subunit 7 | protein | 126 | 65% helix, 0% strand | P00128 |
| H | Cytochrome B-C1 complex subunit 8 | protein | 93 | 43% helix, 5% strand | P08525 |
| I | Cytochrome B-C1 complex subunit 9 | protein | 57 | 72% helix, 0% strand | P22289 |
| J | Igh protein | protein | 127 | 2% helix, 50% strand | — |
| K | Ig kappa chain V-V region hp 124E1 | protein | 107 | 0% helix, 32% strand | — |
Ligands and binding sites
- 3PH · 1,2-diacyl-glycerol-3-sn-phosphate · ligand · 3 copies · chains A, C, E, H, D, I
- HEM · Protoporphyrin IX containing Fe · ligand · 3 copies · chains C, D
- UMQ · Undecyl-maltoside · ligand · chains A, E, H, I
- AOQ · 2-[trans-4-(4-chlorophenyl)cyclohexyl]-3-hydroxynaphthalene-1,4-dione · ligand · chains C
- 3PE · 1,2-diacyl-sn-glycero-3-phosphoethanolamine · ligand · chains C
- UQ6 · 5-(3,7,11,15,19,23-hexamethyl-tetracosa-2,6,10,14,18, 22-hexaenyl)-2,3-dimethoxy-6-methyl-benzene-1,4-diol · ligand · chains C
- FES · Fe2/s2 (inorganic) cluster · ligand · chains E
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 | 693 | 0.82 | 0.86 | 66 | HEM |
| 2 | 166 | 0.82 | 0.97 | 36 | empty |
| 3 | 361 | 0.79 | 0.89 | 43 | empty |
| 4 | 504 | 0.79 | 0.86 | 53 | HEM, UQ6 |
| 5 | 673 | 0.77 | 0.81 | 58 | 3PH |
Interfaces
25 interfaces between chains.
- C–G · 1895 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 1659 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 1577 Ų buried · 18 hydrogen bonds · protein-protein
- C–H · 1449 Ų buried · 12 hydrogen bonds · protein-protein
- D–F · 1157 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 4PD4 · Structural analysis of atovaquone-inhibited cytochrome bc1 complex reveals the molecular… · the same entry in another collection · chain K against K, TM-score 1.00
- P00163 · AlphaFold monomer V2.0 prediction for cytochrome B (P00163) · a predicted model of the same protein · chain C against A, 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 P07256
- Every structure of UniProt P07257
- Every structure of UniProt P00163
- Every structure of UniProt P07143
- Every structure of UniProt P08067
- Every structure of UniProt P00127
- Every structure of UniProt P00128
- Every structure of UniProt P08525
- Every structure of UniProt P22289
- Elsewhere: RCSB PDB 4PD4 · PDBe 4PD4 · UniProt P07256 · UniProt P07257 · UniProt P00163 · UniProt P07143 · UniProt P08067 · UniProt P00127 · UniProt P00128 · UniProt P08525 · UniProt P22289
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