MolNFT v1 · #125746 · protein
Crystal structure of mycobacterium tuberculosis CYP126A1 in complex with 1-(3-(1H-imidazol-1-YL)PROPYL)-3-((3S,5S,7S)-adamantan-1-YL)UREA
5LI7 · Putative cytochrome P450 126: “Crystal structure of mycobacterium tuberculosis CYP126A1 in complex with…”. X-ray diffraction, 2 ligands (HEM, 6XD), 9 pockets (best druggability 0.81). MolNFT v1 #125746 on GenesisL1: 3D structure…
- PDB
- 5LI7
- Type
- protein
- Length
- 745 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative cytochrome P450 126
- EC
- 1.14.-.-
- UniProt
- P9WPN8
- Ligands
- HEM, 6XD
- Pockets
- 9 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative cytochrome P450 126 (EC 1.14.-.-) | protein | 373 | 48% helix, 10% strand | P9WPN8 |
| B | Putative cytochrome P450 126 (EC 1.14.-.-) | protein | 372 | 48% helix, 10% strand | P9WPN8 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- 6XD · 1-(1-adamantyl)-3-(3-imidazol-1-ylpropyl)urea · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 624 | 0.81 | 0.86 | 56 | HEM, 6XD |
| 2 | 637 | 0.81 | 0.86 | 62 | HEM, 6XD |
| 3 | 210 | 0.63 | 0.83 | 32 | empty |
| 4 | 230 | 0.60 | 0.80 | 32 | empty |
| 5 | 88 | 0.50 | 0.83 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 842 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 5LI7 · Crystal structure of Mycobacterium tuberculosis CYP126A1 in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
- P9WPN8 · AlphaFold monomer V2.0 prediction for putative cytochrome P450 126 (P9WPN8) · a predicted model of the same protein · chain B 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 P9WPN8
- Elsewhere: RCSB PDB 5LI7 · PDBe 5LI7 · UniProt P9WPN8
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