Research workbench
1.44 ångström crystal structure of CYP121 from mycobacterium tuberculosis in complex with substrate and cn
Analyse 1.44 ångström crystal structure of CYP121 from mycobacterium tuberculosis in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5WP2
- Type
- protein
- Length
- 394 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mycocyclosin synthase
- EC
- 1.14.21.9
- UniProt
- P9WPP6
- Ligands
- HEM, YTT, SO4, CYN
- Pockets
- 4 · best druggability 0.87
Structure
x-ray diffraction · 1 distinct chain · 52% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mycocyclosin synthase (EC 1.14.21.9) | protein | 394 | 52% helix, 10% strand | P9WPP6 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · chains A
- YTT · (3S,6S)-3,6-bis(4-hydroxybenzyl)piperazine-2,5-dione · ligand · chains A
- SO4 · Sulfate ion · ion · 4 copies · chains A
- CYN · Cyanide ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 844 | 0.87 | 0.89 | 78 | HEM, YTT, CYN |
| 2 | 51 | 0.40 | 0.82 | 18 | empty |
| 3 | 58 | 0.37 | 0.80 | 17 | empty |
| 4 | 51 | 0.26 | 0.73 | 14 | empty |
Compared structures
- 5WP2 · 1.44 Angstrom crystal structure of CYP121 from Mycobacterium tuberculosis in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
- P9WPP6 · AlphaFold monomer V2.0 prediction for mycocyclosin synthase (P9WPP6) · a predicted model of the same protein · chain A 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 P9WPP6
- Elsewhere: RCSB PDB 5WP2 · PDBe 5WP2 · UniProt P9WPP6
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