Research workbench
2.09 ångström resolution structure of a hypoxanthine-guanine phosphoribosyltransferase (hpt-1) from bacillus anthracis str. 'ames ancestor' in complex with gmp
Analyse 2.09 ångström resolution 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
- 3KB8
- Type
- protein
- Length
- 750 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hypoxanthine phosphoribosyltransferase
- EC
- 2.4.2.8
- UniProt
- C3P9L0
- Ligands
- 5GP, GLC, FRU, MG, PO4
- Pockets
- 6 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 29% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hypoxanthine phosphoribosyltransferase (EC 2.4.2.8) | protein | 201 | 28% helix, 35% strand | C3P9L0 |
| B | Hypoxanthine phosphoribosyltransferase (EC 2.4.2.8) | protein | 189 | 29% helix, 30% strand | C3P9L0 |
| C, D | Hypoxanthine phosphoribosyltransferase (EC 2.4.2.8) | protein | 180 | 31% helix, 32% strand | C3P9L0 |
Ligands and binding sites
- 5GP · Guanosine-5'-monophosphate · ligand · 2 copies · chains A, B
- GLC · alpha-D-glucopyranose · sugar · 3 copies · chains C, D
- FRU · beta-D-fructofuranose · sugar · 3 copies · chains A, C, D
- MG · Magnesium ion · metal · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 13 copies · chains A, B, C, D
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1141 | 0.73 | 0.76 | 86 | PO4, 5GP, MG |
| 2 | 432 | 0.61 | 0.76 | 42 | PO4 |
| 3 | 405 | 0.58 | 0.75 | 42 | PO4, 5GP, MG |
| 4 | 72 | 0.46 | 0.82 | 19 | PO4 |
| 5 | 79 | 0.42 | 0.79 | 15 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2242 Ų buried · 33 hydrogen bonds · protein-protein
- C–D · 1742 Ų buried · 20 hydrogen bonds · protein-protein
- B–C · 969 Ų buried · 29 hydrogen bonds · protein-protein
- A–D · 926 Ų buried · 25 hydrogen bonds · protein-protein
- A–C · 239 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 3KB8 · 2.09 Angstrom resolution structure of a hypoxanthine-guanine phosphoribosyltransferase… · 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 C3P9L0
- Elsewhere: RCSB PDB 3KB8 · PDBe 3KB8 · UniProt C3P9L0
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