Research workbench
Crystal structure analysis of the anthranilate phosphoribosyltransferase from erwinia carotovora (current name, pectobacterium carotovorum)
Analyse Crystal structure analysis of the anthranilate phosphoribosyltransferase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1KGZ
- Type
- protein
- Length
- 658 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Anthranilate phosphoribosyltransferase
- EC
- 2.4.2.18
- UniProt
- Q8VP84
- Ligands
- PRP, MN, HG
- Pockets
- 4 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 51% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Anthranilate phosphoribosyltransferase (EC 2.4.2.18) | protein | 328 | 50% helix, 12% strand | Q8VP84 |
| B | Anthranilate phosphoribosyltransferase (EC 2.4.2.18) | protein | 330 | 52% helix, 13% strand | Q8VP84 |
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
- HG · Mercury (II) ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 518 | 0.71 | 0.81 | 56 | MN, PRP |
| 2 | 432 | 0.68 | 0.80 | 51 | MN, PRP |
| 3 | 97 | 0.39 | 0.76 | 13 | empty |
| 4 | 78 | 0.36 | 0.76 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 890 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 1KGZ · Crystal Structure Analysis of the Anthranilate Phosphoribosyltransferase from Erwinia… · 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 Q8VP84
- Elsewhere: RCSB PDB 1KGZ · PDBe 1KGZ · UniProt Q8VP84
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