Research workbench
Crystal structure of E. COLI hypoxanthine phosphoribosyltransferase in complexed with {[(2-[(hypoxanthin-9H-YL)METHYL]PROPANE-1,3-diyl) BIS(OXY)]BIS- (METHYLENE)}DIPHOSPHONIC acid
Analyse Crystal structure of E. COLI hypoxanthine phosphoribosyltransferase in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5KNX
- Type
- protein
- Length
- 349 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hypoxanthine-guanine phosphoribosyltransferase
- UniProt
- A0A0U4JN50
- Ligands
- 6WC, MG
- Pockets
- 3 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 24% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hypoxanthine-guanine phosphoribosyltransferase | protein | 173 | 24% helix, 34% strand | A0A0U4JN50 |
| B | Hypoxanthine-guanine phosphoribosyltransferase | protein | 176 | 24% helix, 32% strand | A0A0U4JN50 |
Ligands and binding sites
- 6WC · [2-[(6-oxidanylidene-1~{H}-purin-9-yl)methyl]-3-(phosphonomethoxy)propoxy]methylphosphonic acid · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 3 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 | 474 | 0.72 | 0.82 | 34 | 6WC, MG |
| 2 | 487 | 0.70 | 0.80 | 39 | 6WC, MG |
| 3 | 233 | 0.58 | 0.79 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 1284 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 5KNX · Crystal structure of E. coli hypoxanthine 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 5KNX · PDBe 5KNX · UniProt A0A0U4JN50
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