MolNFT v1 · #124730 · protein
Crystal structure of E. COLI hypoxanthine phosphoribosyltransferase in complexed with 2-((2,3-DIHYDROXYPROPYL)(2-(hypoxanthin-9-YL)ETHYL) AMINO)ETHYLPHOSPHONIC acid
5KNT · Hypoxanthine-guanine phosphoribosyltransferase: “Crystal structure of E. COLI hypoxanthine phosphoribosyltransferase in complexed with…”. X-ray diffraction, 2 ligands (6WB, MG), 3 pockets (best druggability 0.58). MolNFT v1 #124730…
- PDB
- 5KNT
- 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
- 6WB, MG
- Pockets
- 3 · best druggability 0.58
Structure
x-ray diffraction · 2 distinct chains · 24% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hypoxanthine-guanine phosphoribosyltransferase | protein | 169 | 23% helix, 37% strand | A0A0U4JN50 |
| B | Hypoxanthine-guanine phosphoribosyltransferase | protein | 171 | 25% helix, 35% strand | A0A0U4JN50 |
Ligands and binding sites
- 6WB · 2-[[(2~{S})-2,3-bis(oxidanyl)propyl]-[2-(6-oxidanylidene-1~{H}-purin-9-yl) ethyl]amino]ethylphosphonic acid · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · chains A
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains 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 | 223 | 0.58 | 0.80 | 20 | empty |
| 2 | 342 | 0.57 | 0.76 | 35 | 6WB |
| 3 | 259 | 0.51 | 0.75 | 32 | 6WB, MG |
Interfaces
1 interface between chains.
- A–B · 1251 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 5KNT · 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 5KNT · PDBe 5KNT · UniProt A0A0U4JN50
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