Research workbench
Crystal structure of an anthranilate phosphoribosyltransferase (target id nysgrc-016600) from xanthomonas campestris
Analyse Crystal structure of an anthranilate phosphoribosyltransferase (target id… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4HKM
- Type
- protein
- Length
- 649 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Anthranilate phosphoribosyltransferase
- EC
- 2.4.2.18
- UniProt
- Q8PD71
- Ligands
- PO4
- Pockets
- 7 · best druggability 0.69
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 | 318 | 53% helix, 13% strand | Q8PD71 |
| B | Anthranilate phosphoribosyltransferase (EC 2.4.2.18) | protein | 331 | 54% helix, 14% strand | Q8PD71 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 6 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
- CXS · 3-cyclohexyl-1-propylsulfonic acid · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 514 | 0.69 | 0.79 | 57 | PO4 |
| 2 | 311 | 0.57 | 0.77 | 43 | empty |
| 3 | 95 | 0.53 | 0.84 | 24 | empty |
| 4 | 123 | 0.49 | 0.79 | 14 | PO4 |
| 5 | 124 | 0.48 | 0.79 | 13 | GOL |
Interfaces
1 interface between chains.
- A–B · 279 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 28 modified (engineered).
Compared structures
- 4HKM · Crystal Structure of an Anthranilate Phosphoribosyltransferase (target ID NYSGRC-016600)… · the same entry in another collection · chain A against A, TM-score 1.00
- Q8PD71 · AlphaFold monomer V2.0 prediction for anthranilate phosphoribosyltransferase (Q8PD71) · 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 Q8PD71
- Elsewhere: RCSB PDB 4HKM · PDBe 4HKM · UniProt Q8PD71
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