MolNFT v1 · #92831 · protein
Bianthranilate-like analogue bound in the outer site of anthranilate phosphoribosyltransferase (anprt; trpd)
4GKM: “Bianthranilate-like analogue bound in the outer site of anthranilate phosphoribosyltransferase (anprt; trpd)”. X-ray diffraction, 3 ligands (PRP, 683, MG), 6 pockets (best druggability 0.79). MolNFT v1 #92831 on GenesisL1: 3D…
- PDB
- 4GKM
- Type
- protein
- Length
- 692 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Anthranilate phosphoribosyltransferase
- EC
- 2.4.2.18
- UniProt
- P66992
- Ligands
- PRP, 683, MG
- Pockets
- 6 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 52% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Anthranilate phosphoribosyltransferase (EC 2.4.2.18) | protein | 346 | 52% helix, 12% strand | P66992 |
Ligands and binding sites
- PRP · 1-O-pyrophosphono-5-O-phosphono-alpha-D-ribofuranose · ligand · 2 copies · chains A, B
- 683 · 2-[(2-carboxyphenyl)amino]-5-methylbenzoic acid · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 4 copies · chains A, B
- GOL · Glycerol · additive · 7 copies · chains A, B
- DMS · Dimethyl sulfoxide · additive · 3 copies · chains A, B
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 | 454 | 0.79 | 0.87 | 51 | PRP, MG, 683, GOL |
| 2 | 439 | 0.78 | 0.86 | 50 | PRP, MG, 683, GOL |
| 3 | 74 | 0.41 | 0.80 | 20 | GOL |
| 4 | 67 | 0.38 | 0.79 | 19 | GOL |
| 5 | 73 | 0.31 | 0.74 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 859 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 4GKM · Bianthranilate-like analogue bound in the outer site of anthranilate… · the same entry in another collection · chain A 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 P66992
- Elsewhere: RCSB PDB 4GKM · PDBe 4GKM · UniProt P66992
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