MolNFT v1 · #62567 · protein
Crystal structure of P450BIOI in complex with hexadec-9Z-enoic acid ligated acyl carrier protein
3EJD: “Crystal structure of P450BIOI in complex with hexadec-9Z-enoic acid ligated acyl carrier protein”. X-ray diffraction, 3 ligands (ZMQ, HEM, CL), 20 pockets (best druggability 0.87). MolNFT v1 #62567 on GenesisL1: 3D structure…
- PDB
- 3EJD
- Type
- protein
- Length
- 1,840 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acyl carrier protein; Biotin biosynthesis cytochrome P450-like enzyme
- EC
- 1.14.-.-
- UniProt
- P0A6A8, P53554
- Ligands
- ZMQ, HEM, CL
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 6 distinct chains · 56% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Acyl carrier protein | protein | 78 | 53% helix, 3% strand | P0A6A8 |
| B | Biotin biosynthesis cytochrome P450-like enzyme (EC 1.14.-.-) | protein | 382 | 57% helix, 11% strand | P53554 |
| C, G | Acyl carrier protein | protein | 77 | 51% helix, 3% strand | P0A6A8 |
| D | Biotin biosynthesis cytochrome P450-like enzyme (EC 1.14.-.-) | protein | 385 | 57% helix, 11% strand | P53554 |
| F | Biotin biosynthesis cytochrome P450-like enzyme (EC 1.14.-.-) | protein | 381 | 57% helix, 11% strand | P53554 |
| H | Biotin biosynthesis cytochrome P450-like enzyme (EC 1.14.-.-) | protein | 382 | 56% helix, 11% strand | P53554 |
Ligands and binding sites
- ZMQ · S-[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] (9Z)-hexadec-9-enethioate · ligand · 4 copies · chains A, B, C, D, E, F, G, H
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains B, D, F, H
- CL · Chloride ion · ion · 2 copies · chains B, F
- HTG · heptyl 1-thio-beta-D-glucopyranoside · additive · 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, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 884 | 0.87 | 0.88 | 100 | ZMQ, HTG, HEM |
| 2 | 908 | 0.86 | 0.88 | 92 | ZMQ, HTG, HEM |
| 3 | 882 | 0.86 | 0.88 | 95 | ZMQ, HTG, HEM |
| 4 | 850 | 0.86 | 0.87 | 91 | ZMQ, HTG, HEM |
| 5 | 981 | 0.82 | 0.84 | 80 | empty |
Interfaces
8 interfaces between chains.
- B–D · 798 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 641 Ų buried · 11 hydrogen bonds · protein-protein
- G–H · 624 Ų buried · 12 hydrogen bonds · protein-protein
- E–F · 614 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 611 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 3EJD · Crystal Structure of P450BioI in complex with hexadec-9Z-enoic acid ligated Acyl Carrier… · the same entry in another collection · chain H against H, TM-score 1.00
- P53554 · AlphaFold monomer V2.0 prediction for biotin biosynthesis cytochrome P450 (P53554) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 P0A6A8
- Every structure of UniProt P53554
- Elsewhere: RCSB PDB 3EJD · PDBe 3EJD · UniProt P0A6A8 · UniProt P53554
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