MolNFT v1 · #124731 · protein
Crystal structure of E. COLI hypoxanthine phosphoribosyltransferase in complexed with 9-[N,N-(bis-3-PHOSPHONOPROPYL)AMINOMETHYL]-9- deazahypoxanthine
5KNU · Hypoxanthine-guanine phosphoribosyltransferase: “Crystal structure of E. COLI hypoxanthine phosphoribosyltransferase in complexed with…”. X-ray diffraction, 2 ligands (6WA, MG), 3 pockets (best druggability 0.63). MolNFT v1 #124731…
- PDB
- 5KNU
- Type
- protein
- Length
- 345 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hypoxanthine-guanine phosphoribosyltransferase
- UniProt
- A0A0U4JN50
- Ligands
- 6WA, MG
- Pockets
- 3 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 24% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hypoxanthine-guanine phosphoribosyltransferase | protein | 172 | 24% helix, 34% strand | A0A0U4JN50 |
| B | Hypoxanthine-guanine phosphoribosyltransferase | protein | 173 | 25% helix, 34% strand | A0A0U4JN50 |
Ligands and binding sites
- 6WA · 3-[(4-oxidanylidene-3,5-dihydropyrrolo[3,2-d]pyrimidin-7-yl)methyl-(3-phosphonopropyl)amino]propylphosphonic acid · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains A
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 | 439 | 0.63 | 0.77 | 39 | 6WA, MG |
| 2 | 222 | 0.59 | 0.80 | 21 | empty |
| 3 | 330 | 0.57 | 0.76 | 30 | 6WA, MG |
Interfaces
1 interface between chains.
- A–B · 1295 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 5KNU · 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 5KNU · PDBe 5KNU · UniProt A0A0U4JN50
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