Research workbench
Mycobacterium tuberculosis cysm in complex with the urea-scaffold inhibitor 2 [3-(3-([1,1'-biphenyl]-3-YL)UREIDO)BENZOIC acid]
Analyse Mycobacterium tuberculosis cysm in complex with the urea-scaffold inhibitor 2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5I7R
- Type
- protein
- Length
- 622 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- O-phosphoserine sulfhydrylase
- EC
- 2.5.1.113
- UniProt
- P9WP53
- Ligands
- PLP, 68W
- Pockets
- 5 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | O-phosphoserine sulfhydrylase (EC 2.5.1.113) | protein | 316 | 42% helix, 20% strand | P9WP53 |
| A | O-phosphoserine sulfhydrylase (EC 2.5.1.113) | protein | 306 | 46% helix, 19% strand | P9WP53 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains B, A
- 68W · 3-{[([1,1'-biphenyl]-3-yl)carbamoyl]amino}benzoic acid · ligand · 2 copies · chains B, A
- ACT · Acetate ion · additive · 5 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 846 | 0.83 | 0.85 | 86 | PLP, 68W, ACT |
| 2 | 109 | 0.78 | 0.98 | 35 | ACT |
| 3 | 670 | 0.74 | 0.80 | 60 | PLP, 68W |
| 4 | 136 | 0.50 | 0.80 | 23 | empty |
| 5 | 55 | 0.27 | 0.74 | 14 | empty |
Interfaces
1 interface between chains.
- B–A · 2079 Ų buried · 37 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 5I7R · Mycobacterium tuberculosis CysM in complex with the Urea-scaffold inhibitor 2… · the same entry in another collection · chain B against B, TM-score 1.00
- P9WP53 · AlphaFold monomer V2.0 prediction for O-phosphoserine sulfhydrylase (P9WP53) · a predicted model of the same protein · chain A 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 5I7R · PDBe 5I7R · UniProt P9WP53
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