MolNFT v1 · #115040 · protein
Prpp complexed with two MN2+ in the active site of mycobacterium tuberculosis anthranilate phosphoribosyltransferase (anprt; trpd)
5C7S: “Prpp complexed with two MN2+ in the active site of mycobacterium tuberculosis anthranilate…”. X-ray diffraction, 2 ligands (PRP, MN), 5 pockets (best druggability 0.79). MolNFT v1 #115040 on GenesisL1: 3D structure, binding sites…
- PDB
- 5C7S
- Type
- protein
- Length
- 687 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
- PRP, MN
- Pockets
- 5 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 53% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Anthranilate phosphoribosyltransferase (EC 2.4.2.18) | protein | 344 | 53% helix, 13% strand | P9WFX5 |
| B | Anthranilate phosphoribosyltransferase (EC 2.4.2.18) | protein | 343 | 52% helix, 13% strand | P9WFX5 |
Ligands and binding sites
- PRP · 1-O-pyrophosphono-5-O-phosphono-alpha-D-ribofuranose · ligand · 2 copies · chains A, B
- MN · Manganese (II) ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 443 | 0.79 | 0.87 | 52 | MN, PRP |
| 2 | 385 | 0.77 | 0.87 | 52 | MN, PRP |
| 3 | 77 | 0.34 | 0.76 | 18 | empty |
| 4 | 62 | 0.34 | 0.77 | 14 | empty |
| 5 | 64 | 0.30 | 0.74 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 866 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 5C7S · PRPP complexed with two Mn2+ in the active site of Mycobacterium tuberculosis… · 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 A 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 P9WFX5
- Elsewhere: RCSB PDB 5C7S · PDBe 5C7S · UniProt P9WFX5
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