Research workbench
Human hypoxanthine guanine phosphoribosyltransferase in complex with [3R,4R]-4-guanin-9-yl-3-((R)-2-hydroxy-2-PHOSPHONOETHYL)OXY-1-N- (PHOSPHONOPROPIONYL)PYRROLIDINE
Analyse Human hypoxanthine guanine phosphoribosyltransferase in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6BNJ
- Type
- protein
- Length
- 816 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hypoxanthine-guanine phosphoribosyltransferase
- EC
- 2.4.2.8
- UniProt
- P00492
- Ligands
- WPG, MG
- Pockets
- 10 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 30% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hypoxanthine-guanine phosphoribosyltransferase (EC 2.4.2.8) | protein | 197 | 29% helix, 29% strand | P00492 |
| B | Hypoxanthine-guanine phosphoribosyltransferase (EC 2.4.2.8) | protein | 207 | 30% helix, 30% strand | P00492 |
| C | Hypoxanthine-guanine phosphoribosyltransferase (EC 2.4.2.8) | protein | 204 | 31% helix, 28% strand | P00492 |
| D | Hypoxanthine-guanine phosphoribosyltransferase (EC 2.4.2.8) | protein | 208 | 30% helix, 29% strand | P00492 |
Ligands and binding sites
- WPG · (3-{(3R,4R)-3-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)-4-[(2R)-2-hydroxy-2-phosphonoethoxy]pyrrolidin-1-yl}-3-oxopropyl)phosphonic acid · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1094 | 0.84 | 0.85 | 81 | empty |
| 2 | 167 | 0.55 | 0.80 | 32 | empty |
| 3 | 288 | 0.54 | 0.76 | 29 | WPG, MG |
| 4 | 238 | 0.50 | 0.75 | 26 | WPG, MG |
| 5 | 149 | 0.50 | 0.78 | 34 | empty |
Interfaces
6 interfaces between chains.
- B–D · 1705 Ų buried · 27 hydrogen bonds · protein-protein
- A–C · 1662 Ų buried · 30 hydrogen bonds · protein-protein
- C–D · 902 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 869 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 363 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 6BNJ · Human hypoxanthine guanine phosphoribosyltransferase in complex 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 P00492
- Elsewhere: RCSB PDB 6BNJ · PDBe 6BNJ · UniProt P00492
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