MolNFT v1 · #122667 · protein
Mycobacterium tuberculosis cysm in complex with the urea-scaffold inhibitor 4 [5-(3-([1,1'-biphenyl]-3-YL)UREIDO)-2-hydroxybenzoic acid]
5IW8 · O-phosphoserine sulfhydrylase: “Mycobacterium tuberculosis cysm in complex with the urea-scaffold inhibitor 4…”. X-ray diffraction, 3 ligands (6EC, PLP, NA), 8 pockets (best druggability 0.84). MolNFT v1 #122667 on GenesisL1: 3D…
- PDB
- 5IW8
- Type
- protein
- Length
- 614 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
- 6EC, PLP, NA
- Pockets
- 8 · best druggability 0.84
Structure
x-ray diffraction · 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 | 299 | 44% helix, 20% strand | P9WP53 |
| B | O-phosphoserine sulfhydrylase (EC 2.5.1.113) | protein | 315 | 41% helix, 19% strand | P9WP53 |
Ligands and binding sites
- 6EC · 5-{[([1,1'-biphenyl]-3-yl)carbamoyl]amino}-2-hydroxybenzoic acid · ligand · 2 copies · chains A, B
- PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 426 | 0.84 | 0.92 | 56 | 6EC, PLP |
| 2 | 98 | 0.76 | 0.97 | 26 | empty |
| 3 | 659 | 0.72 | 0.79 | 78 | 6EC, PLP |
| 4 | 95 | 0.50 | 0.83 | 23 | empty |
| 5 | 146 | 0.48 | 0.78 | 29 | empty |
Interfaces
1 interface between chains.
- A–B · 1968 Ų buried · 34 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 5IW8 · Mycobacterium tuberculosis CysM in complex with the Urea-scaffold inhibitor 4… · 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 0.95
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 5IW8 · PDBe 5IW8 · UniProt P9WP53
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