Research workbench
Crystal structure of hypoxanthine phosphoribosyltransferase from brachybacterium faecium dsm 4810, nysgrc target 029763.
Analyse Crystal structure of hypoxanthine phosphoribosyltransferase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4PFQ
- Type
- protein
- Length
- 1,445 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hypoxanthine phosphoribosyltransferase
- EC
- 2.4.2.8
- UniProt
- C7MC15
- Ligands
- MG
- Pockets
- 16 · best druggability 0.68
Structure
x-ray diffraction · 3 distinct chains · 27% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, G | Hypoxanthine phosphoribosyltransferase (EC 2.4.2.8) | protein | 177 | 27% helix, 33% strand | C7MC15 |
| C, E, F, H | Hypoxanthine phosphoribosyltransferase (EC 2.4.2.8) | protein | 184 | 26% helix, 29% strand | C7MC15 |
| D | Hypoxanthine phosphoribosyltransferase (EC 2.4.2.8) | protein | 178 | 29% helix, 33% strand | C7MC15 |
Ligands and binding sites
- MG · Magnesium ion · metal · 12 copies · chains A, B, D, C, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 508 | 0.68 | 0.79 | 64 | MG |
| 2 | 434 | 0.68 | 0.80 | 57 | MG |
| 3 | 384 | 0.63 | 0.78 | 45 | MG |
| 4 | 194 | 0.63 | 0.84 | 22 | empty |
| 5 | 205 | 0.63 | 0.83 | 22 | empty |
Interfaces
14 interfaces between chains.
- B–C · 1356 Ų buried · 12 hydrogen bonds · protein-protein
- D–F · 1348 Ų buried · 13 hydrogen bonds · protein-protein
- A–H · 1314 Ų buried · 13 hydrogen bonds · protein-protein
- E–G · 1311 Ų buried · 14 hydrogen bonds · protein-protein
- C–E · 827 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 32 modified (engineered).
Compared structures
- 4PFQ · Crystal structure of hypoxanthine phosphoribosyltransferase from Brachybacterium faecium… · 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 C7MC15
- Elsewhere: RCSB PDB 4PFQ · PDBe 4PFQ · UniProt C7MC15
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