Research workbench
Mycobacterium tuberculosis CysM in complex with the Urea-scaffold inhibitor 3 [4-(3-([1,1'-Biphenyl]-3-yl)ureido)-2-hydroxybenzoic acid]
Analyse Mycobacterium tuberculosis CysM in complex with the Urea-scaffold inhibitor 3… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5IWC
- Type
- protein
- Length
- 592 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.7
- Source
- Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
- Molecule
- O-phosphoserine sulfhydrylase
- EC
- 2.5.1.113
- UniProt
- P9WP53
- Ligands
- PLP, 6EQ
- Pockets
- 6 · best druggability 0.79
Structure
x-ray diffraction · resolution 2.7 · 2 distinct chains · 43% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | O-phosphoserine sulfhydrylase (EC 2.5.1.113) | protein | 297 | 44% helix, 21% strand | P9WP53 |
| B | O-phosphoserine sulfhydrylase (EC 2.5.1.113) | protein | 295 | 42% helix, 20% strand | P9WP53 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B
- 6EQ · 4-{[([1,1'-biphenyl]-3-yl)carbamoyl]amino}-2-hydroxybenzoic acid · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 126 | 0.79 | 0.97 | 33 | empty |
| 2 | 974 | 0.78 | 0.80 | 116 | PLP, 6EQ |
| 3 | 119 | 0.52 | 0.82 | 20 | empty |
| 4 | 64 | 0.31 | 0.75 | 14 | empty |
| 5 | 53 | 0.26 | 0.73 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 2092 Ų buried · 27 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 5IWC · Mycobacterium tuberculosis cysm in complex with the urea-scaffold inhibitor 3… · the same entry in another collection · chain A against A, TM-score 1.00
- P9WP53 · AlphaFold monomer V2.0 prediction for O-phosphoserine sulfhydrylase (P9WP53) · a predicted model of the same protein · chain B against A, TM-score 0.97
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 P9WP53
- Elsewhere: RCSB PDB 5IWC · PDBe 5IWC · UniProt P9WP53
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