Research workbench
Crystal structure mycobacterium tuberculosis CYP121 in complex with inhibitor fragment 24A
Analyse Crystal structure mycobacterium tuberculosis CYP121 in complex with inhibitor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5IBD
- 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, GGJ, SO4
- Pockets
- 2 · best druggability 0.87
Structure
x-ray diffraction · 1 distinct chain · 51% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mycocyclosin synthase (EC 1.14.21.9) | protein | 394 | 51% helix, 10% strand | P9WPP6 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · chains A
- GGJ · 4-(3'-amino[1,1'-biphenyl]-3-yl)-3-(4-methoxyphenyl)-1H-pyrazol-5-amine · ligand · chains A
- SO4 · Sulfate ion · ion · 5 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 911 | 0.87 | 0.89 | 86 | SO4, HEM, GGJ |
| 2 | 51 | 0.27 | 0.74 | 15 | empty |
Compared structures
- 5IBD · Crystal structure Mycobacterium tuberculosis CYP121 in complex with inhibitor fragment 24a · 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 5IBD · PDBe 5IBD · UniProt P9WPP6
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