Research workbench
E COLI hypoxanthine guanine phosphoribosyltransferase in complexed with 9-[(N-phosphonoethyl-N-phosphonobutyl)-2-aminoethyl]- hypoxanthine
Analyse E COLI hypoxanthine guanine phosphoribosyltransferase in complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5KNV
- Type
- protein
- Length
- 340 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hypoxanthine-guanine phosphoribosyltransferase
- UniProt
- A0A0U4JN50
- Ligands
- 6W9, MG
- Pockets
- 3 · best druggability 0.58
Structure
x-ray diffraction · 2 distinct chains · 24% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hypoxanthine-guanine phosphoribosyltransferase | protein | 169 | 24% helix, 33% strand | A0A0U4JN50 |
| B | Hypoxanthine-guanine phosphoribosyltransferase | protein | 171 | 24% helix, 33% strand | A0A0U4JN50 |
Ligands and binding sites
- 6W9 · 2-[2-(6-oxidanylidene-1~{H}-purin-9-yl)ethyl-(4-phosphonobutyl)amino]ethylphosphonic acid · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 213 | 0.58 | 0.80 | 19 | empty |
| 2 | 307 | 0.56 | 0.76 | 29 | 6W9, MG |
| 3 | 278 | 0.56 | 0.77 | 30 | 6W9, MG |
Interfaces
1 interface between chains.
- A–B · 1298 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 5KNV · E coli hypoxanthine guanine phosphoribosyltransferase in complexed with… · 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 A0A0U4JN50
- Elsewhere: RCSB PDB 5KNV · PDBe 5KNV · UniProt A0A0U4JN50
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