Research workbench
Stereoisomer of prpp bound in the active site of mycobacterium tuberculosis anthranilate phosphoribosyl (anprt; trpd)
Analyse Stereoisomer of prpp bound in the active site of mycobacterium tuberculosis… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5C1R
- Type
- protein
- Length
- 689 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Anthranilate phosphoribosyltransferase
- EC
- 2.4.2.18
- UniProt
- P9WFX5
- Ligands
- 51N, MG
- Pockets
- 6 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 53% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Anthranilate phosphoribosyltransferase (EC 2.4.2.18) | protein | 343 | 53% helix, 13% strand | P9WFX5 |
| B | Anthranilate phosphoribosyltransferase (EC 2.4.2.18) | protein | 346 | 53% helix, 12% strand | P9WFX5 |
Ligands and binding sites
- 51N · 5-O-[(R)-hydroxy(phosphonooxy)phosphoryl]-1-O-phosphono-alpha-D-ribofuranose · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 4 copies · chains A, B
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 434 | 0.78 | 0.87 | 50 | MG, 51N |
| 2 | 480 | 0.76 | 0.85 | 52 | MG, 51N |
| 3 | 50 | 0.38 | 0.81 | 15 | empty |
| 4 | 56 | 0.37 | 0.79 | 15 | empty |
| 5 | 53 | 0.32 | 0.76 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 875 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 5C1R · Stereoisomer of PRPP bound in the active site of Mycobacterium tuberculosis anthranilate… · the same entry in another collection · chain A against A, TM-score 1.00
- P9WFX5 · AlphaFold monomer V2.0 prediction for anthranilate phosphoribosyltransferase (P9WFX5) · a predicted model of the same protein · chain B against A, TM-score 1.00
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 P9WFX5
- Elsewhere: RCSB PDB 5C1R · PDBe 5C1R · UniProt P9WFX5
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