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1.95 ångström resolution crystal structure of a hypoxanthine-guanine phosphoribosyltransferase (hpt-2) from bacillus anthracis str. 'ames ancestor' with hepes molecule in the active site
Analyse 1.95 ångström resolution crystal structure of a hypoxanthine-guanine… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4QYI
- Type
- protein
- Length
- 850 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hypoxanthine phosphoribosyltransferase
- EC
- 2.4.2.8
- UniProt
- Q81KC7
- Ligands
- MG, PO4
- Pockets
- 6 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 26% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hypoxanthine phosphoribosyltransferase (EC 2.4.2.8) | protein | 170 | 27% helix, 35% strand | Q81KC7 |
| B, C | Hypoxanthine phosphoribosyltransferase | protein | 171 | 27% helix, 35% strand | Q81KC7 |
| D | Hypoxanthine phosphoribosyltransferase | protein | 169 | 27% helix, 36% strand | Q81KC7 |
| E | Hypoxanthine phosphoribosyltransferase | protein | 169 | 24% helix, 36% strand | Q81KC7 |
Ligands and binding sites
- MG · Magnesium ion · metal · 9 copies · chains A, B, C, D, E
- PO4 · Phosphate ion · ion · 8 copies · chains A, B, C, D, E
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 3 copies · chains B, C, E
- GOL · Glycerol · additive · chains E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1092 | 0.74 | 0.77 | 99 | MG, PO4, EPE |
| 2 | 875 | 0.72 | 0.77 | 83 | MG, PO4 |
| 3 | 188 | 0.55 | 0.79 | 19 | empty |
| 4 | 282 | 0.53 | 0.75 | 32 | MG, PO4, EPE |
| 5 | 147 | 0.49 | 0.79 | 20 | empty |
Interfaces
4 interfaces between chains.
- A–D · 1253 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 1230 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 813 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 793 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (artifact).
Compared structures
- 4QYI · 1.95 Angstrom resolution crystal structure of a hypoxanthine-guanine… · 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 Q81KC7
- Elsewhere: RCSB PDB 4QYI · PDBe 4QYI · UniProt Q81KC7
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