MolNFT v1 · #76986 · protein
Closed crystal structure of cytochrome P450 2B4 covalently bound to the mechanism-based inactivator tert-butylphenylacetylene
3R1A: “Closed crystal structure of cytochrome P450 2B4 covalently bound to the mechanism-based inactivator…”. X-ray diffraction, 2 ligands (HEM, TB2), 20 pockets (best druggability 0.88). MolNFT v1 #76986 on GenesisL1: 3D structure…
- PDB
- 3R1A
- Type
- protein
- Length
- 3,719 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome P450 2B4
- EC
- 1.14.14.1
- UniProt
- P00178
- Ligands
- HEM, TB2
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G | Cytochrome P450 2B4 (EC 1.14.14.1) | protein | 465 | 51% helix, 10% strand | P00178 |
| H | Cytochrome P450 2B4 (EC 1.14.14.1) | protein | 464 | 42% helix, 9% strand | P00178 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- TB2 · (4-tert-butylphenyl)acetaldehyde · ligand · 8 copies · chains A, B, C, D, E, F, G, H
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 | 512 | 0.88 | 0.94 | 54 | HEM, TB2 |
| 2 | 526 | 0.87 | 0.93 | 53 | HEM, TB2 |
| 3 | 535 | 0.87 | 0.93 | 54 | HEM, TB2 |
| 4 | 617 | 0.87 | 0.91 | 62 | HEM, TB2 |
| 5 | 516 | 0.87 | 0.93 | 52 | HEM, TB2 |
Interfaces
13 interfaces between chains.
- B–E · 541 Ų buried · 4 hydrogen bonds · protein-protein
- D–G · 523 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 471 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 461 Ų buried · 7 hydrogen bonds · protein-protein
- G–H · 446 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 8 covalent (covalent ligand).
Compared structures
- 3R1A · Closed crystal structure of cytochrome P450 2B4 covalently bound to the mechanism-based… · the same entry in another collection · chain H against H, TM-score 1.00
- P00178 · AlphaFold monomer V2.0 prediction for cytochrome P450 2B4 (P00178) · a predicted model of the same protein · chain H against A, TM-score 0.99
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 P00178
- Elsewhere: RCSB PDB 3R1A · PDBe 3R1A · UniProt P00178
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