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Crystal structure of hypoxanthine phosphoribosyltransferase from shewanella pealeana atcc 700345, nysgrc target 029677.
Analyse Crystal structure of hypoxanthine phosphoribosyltransferase from shewanella… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4LYY
- Type
- protein
- Length
- 665 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hypoxanthine phosphoribosyltransferase
- EC
- 2.4.2.8
- UniProt
- A8H0C8
- Ligands
- PO4
- Pockets
- 8 · best druggability 0.55
Structure
x-ray diffraction · 4 distinct chains · 24% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hypoxanthine phosphoribosyltransferase (EC 2.4.2.8) | protein | 171 | 23% helix, 35% strand | A8H0C8 |
| B | Hypoxanthine phosphoribosyltransferase (EC 2.4.2.8) | protein | 164 | 24% helix, 36% strand | A8H0C8 |
| C | Hypoxanthine phosphoribosyltransferase (EC 2.4.2.8) | protein | 164 | 24% helix, 35% strand | A8H0C8 |
| D | Hypoxanthine phosphoribosyltransferase (EC 2.4.2.8) | protein | 166 | 24% helix, 36% strand | A8H0C8 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 2 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 293 | 0.55 | 0.76 | 30 | PO4 |
| 2 | 236 | 0.54 | 0.77 | 27 | PO4 |
| 3 | 247 | 0.53 | 0.76 | 28 | empty |
| 4 | 132 | 0.51 | 0.80 | 20 | empty |
| 5 | 171 | 0.50 | 0.78 | 18 | empty |
Interfaces
4 interfaces between chains.
- C–D · 1293 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1283 Ų buried · 15 hydrogen bonds · protein-protein
- B–D · 833 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 768 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 21 modified (engineered).
Compared structures
- 4LYY · Crystal structure of hypoxanthine phosphoribosyltransferase from Shewanella pealeana ATCC… · the same entry in another collection · chain C against C, 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 A8H0C8
- Elsewhere: RCSB PDB 4LYY · PDBe 4LYY · UniProt A8H0C8
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