Research workbench
Human hgprt in complex with (S)-hpepg, an acyclic nucleoside phosphonate
Analyse Human hgprt in complex with (S)-hpepg, an acyclic nucleoside phosphonate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5BSK
- Type
- protein
- Length
- 762 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
- 4X7, MG
- Pockets
- 11 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 32% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hypoxanthine-guanine phosphoribosyltransferase (EC 2.4.2.8) | protein | 192 | 30% helix, 28% strand | P00492 |
| B | Hypoxanthine-guanine phosphoribosyltransferase (EC 2.4.2.8) | protein | 191 | 31% helix, 29% strand | P00492 |
| C | Hypoxanthine-guanine phosphoribosyltransferase (EC 2.4.2.8) | protein | 191 | 30% helix, 30% strand | P00492 |
| D | Hypoxanthine-guanine phosphoribosyltransferase (EC 2.4.2.8) | protein | 188 | 35% helix, 30% strand | P00492 |
Ligands and binding sites
- 4X7 · (2-{[(2S)-1-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)-3-hydroxypropan-2-yl]oxy}ethyl)phosphonic acid · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1066 | 0.77 | 0.79 | 95 | empty |
| 2 | 92 | 0.64 | 0.90 | 27 | empty |
| 3 | 64 | 0.60 | 0.90 | 25 | empty |
| 4 | 251 | 0.57 | 0.78 | 30 | empty |
| 5 | 237 | 0.51 | 0.75 | 34 | empty |
Interfaces
6 interfaces between chains.
- A–C · 1428 Ų buried · 25 hydrogen bonds · protein-protein
- B–D · 1426 Ų buried · 20 hydrogen bonds · protein-protein
- A–D · 811 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 797 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 51 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5BSK · Human HGPRT in complex with (S)-HPEPG, an acyclic nucleoside phosphonate · 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 5BSK · PDBe 5BSK · UniProt P00492
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