MolNFT v1 · #121848 · protein
Mycobacterium tuberculosis cysm in complex with the urea-scaffold inhibitor 6 [3-(3-(4-BROMOPHENYL)UREIDO)BENZOIC acid]
5I7H · O-phosphoserine sulfhydrylase: “Mycobacterium tuberculosis cysm in complex with the urea-scaffold inhibitor 6…”. X-ray diffraction, 3 ligands (68V, PLP, CL), 13 pockets (best druggability 0.81). MolNFT v1 #121848 on GenesisL1: 3D…
- PDB
- 5I7H
- Type
- protein
- Length
- 1,159 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- O-phosphoserine sulfhydrylase
- EC
- 2.5.1.113
- UniProt
- P9WP53
- Ligands
- 68V, PLP, CL
- Pockets
- 13 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 42% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | O-phosphoserine sulfhydrylase (EC 2.5.1.113) | protein | 280 | 42% helix, 20% strand | P9WP53 |
| B | O-phosphoserine sulfhydrylase (EC 2.5.1.113) | protein | 291 | 44% helix, 21% strand | P9WP53 |
| C | O-phosphoserine sulfhydrylase (EC 2.5.1.113) | protein | 284 | 43% helix, 20% strand | P9WP53 |
| D | O-phosphoserine sulfhydrylase (EC 2.5.1.113) | protein | 304 | 40% helix, 20% strand | P9WP53 |
Ligands and binding sites
- 68V · 3-{[(4-bromophenyl)carbamoyl]amino}benzoic acid · ligand · 4 copies · chains A, B, C, D
- PLP · Pyridoxal-5'-phosphate · ligand · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 178 | 0.81 | 0.96 | 36 | 68V, PLP |
| 2 | 120 | 0.80 | 0.98 | 36 | empty |
| 3 | 105 | 0.78 | 0.97 | 36 | empty |
| 4 | 545 | 0.70 | 0.79 | 53 | 68V, PLP |
| 5 | 452 | 0.66 | 0.79 | 45 | 68V, PLP |
Interfaces
4 interfaces between chains.
- C–D · 2037 Ų buried · 34 hydrogen bonds · protein-protein
- A–B · 2013 Ų buried · 33 hydrogen bonds · protein-protein
- A–D · 343 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 174 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 5I7H · Mycobacterium tuberculosis CysM in complex with the Urea-scaffold inhibitor 6… · the same entry in another collection · chain D against D, TM-score 1.00
- P9WP53 · AlphaFold monomer V2.0 prediction for O-phosphoserine sulfhydrylase (P9WP53) · a predicted model of the same protein · chain C 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 P9WP53
- Elsewhere: RCSB PDB 5I7H · PDBe 5I7H · UniProt P9WP53
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