Research workbench
Mycobacterium tuberculosis cysm in complex with the urea-scaffold inhibitor 5 [3-(3-(P-TOLYL)UREIDO) benzoic acid]
Analyse Mycobacterium tuberculosis cysm in complex with the urea-scaffold inhibitor 5… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5I6D
- Type
- protein
- Length
- 1,180 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
- PLP, AU6
- Pockets
- 13 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 43% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | O-phosphoserine sulfhydrylase (EC 2.5.1.113) | protein | 285 | 43% helix, 20% strand | P9WP53 |
| B | O-phosphoserine sulfhydrylase (EC 2.5.1.113) | protein | 287 | 45% helix, 21% strand | P9WP53 |
| C | O-phosphoserine sulfhydrylase (EC 2.5.1.113) | protein | 290 | 44% helix, 20% strand | P9WP53 |
| D | O-phosphoserine sulfhydrylase (EC 2.5.1.113) | protein | 318 | 41% helix, 19% strand | P9WP53 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 4 copies · chains A, B, C, D
- AU6 · 3-{[(4-methylphenyl)carbamoyl]amino}benzoic acid · ligand · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 186 | 0.82 | 0.96 | 38 | PLP, AU6 |
| 2 | 106 | 0.78 | 0.98 | 37 | empty |
| 3 | 114 | 0.78 | 0.97 | 35 | empty |
| 4 | 520 | 0.70 | 0.79 | 50 | PLP, AU6, GOL |
| 5 | 409 | 0.66 | 0.79 | 44 | PLP, AU6, GOL |
Interfaces
4 interfaces between chains.
- C–D · 2063 Ų buried · 32 hydrogen bonds · protein-protein
- A–B · 2062 Ų buried · 29 hydrogen bonds · protein-protein
- A–D · 438 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 219 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 5I6D · Mycobacterium tuberculosis CysM in complex with the Urea-scaffold inhibitor 5… · 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 5I6D · PDBe 5I6D · UniProt P9WP53
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