Research workbench
Mycobacterium tuberculosis cysm in complex with the urea-scaffold inhibitor 1 [3-(3-(3,4-DICHLOROPHENYL)UREIDO)BENZOIC acid]
Analyse Mycobacterium tuberculosis cysm in complex with the urea-scaffold inhibitor 1… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5I7A
- Type
- protein
- Length
- 1,163 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
- P9WP52
- Ligands
- 68Q, PLP
- Pockets
- 16 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 42% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | O-phosphoserine sulfhydrylase (EC 2.5.1.113) | protein | 281 | 43% helix, 21% strand | P9WP52 |
| B | O-phosphoserine sulfhydrylase (EC 2.5.1.113) | protein | 292 | 43% helix, 21% strand | P9WP52 |
| C | O-phosphoserine sulfhydrylase (EC 2.5.1.113) | protein | 283 | 43% helix, 20% strand | P9WP52 |
| D | O-phosphoserine sulfhydrylase (EC 2.5.1.113) | protein | 307 | 40% helix, 21% strand | P9WP52 |
Ligands and binding sites
- 68Q · 3-{[(3,4-dichlorophenyl)carbamoyl]amino}benzoic acid · ligand · 4 copies · chains A, B, C, D
- PLP · Pyridoxal-5'-phosphate · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 184 | 0.81 | 0.96 | 38 | 68Q, PLP |
| 2 | 125 | 0.79 | 0.97 | 35 | empty |
| 3 | 114 | 0.79 | 0.98 | 32 | empty |
| 4 | 528 | 0.70 | 0.79 | 54 | 68Q, PLP |
| 5 | 400 | 0.64 | 0.78 | 41 | 68Q, PLP |
Interfaces
4 interfaces between chains.
- C–D · 2063 Ų buried · 32 hydrogen bonds · protein-protein
- A–B · 2029 Ų buried · 32 hydrogen bonds · protein-protein
- A–D · 425 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 134 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 5I7A · Mycobacterium tuberculosis CysM in complex with the Urea-scaffold inhibitor 1… · the same entry in another collection · chain C against C, TM-score 1.00
- P9WP52 · AlphaFold monomer V2.0 prediction for O-phosphoserine sulfhydrylase (P9WP52) · 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 P9WP52
- Elsewhere: RCSB PDB 5I7A · PDBe 5I7A · UniProt P9WP52
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