Research workbench
Human hgprt in complex with [(2-[(guanin-9-YL)METHYL]PROPANE-1,3- DIYL)BIS(OXY)]BIS(METHYLENE)DIPHOSPHONIC acid
Analyse Human hgprt in complex with [(2-[(guanin-9-YL)METHYL]PROPANE-1,3… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5W8V
- Type
- protein
- Length
- 819 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
- 9YP, MG
- Pockets
- 7 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 30% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hypoxanthine-guanine phosphoribosyltransferase (EC 2.4.2.8) | protein | 206 | 31% helix, 30% strand | P00492 |
| B | Hypoxanthine-guanine phosphoribosyltransferase (EC 2.4.2.8) | protein | 204 | 30% helix, 31% strand | P00492 |
| C | Hypoxanthine-guanine phosphoribosyltransferase (EC 2.4.2.8) | protein | 205 | 30% helix, 30% strand | P00492 |
| D | Hypoxanthine-guanine phosphoribosyltransferase (EC 2.4.2.8) | protein | 204 | 31% helix, 29% strand | P00492 |
Ligands and binding sites
- 9YP · {[(2R)-2-[(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl) methyl]-3-(2-phosphonoethoxy)propoxy]methyl}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
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1154 | 0.83 | 0.85 | 99 | empty |
| 2 | 164 | 0.55 | 0.80 | 33 | empty |
| 3 | 275 | 0.55 | 0.76 | 39 | 9YP, MG |
| 4 | 167 | 0.52 | 0.78 | 33 | empty |
| 5 | 205 | 0.47 | 0.74 | 26 | 9YP, MG |
Interfaces
6 interfaces between chains.
- B–D · 1707 Ų buried · 30 hydrogen bonds · protein-protein
- A–C · 1698 Ų buried · 32 hydrogen bonds · protein-protein
- C–D · 846 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 843 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 335 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5W8V · HUMAN HGPRT in complex with [(2-[(guanin-9-yl)methyl]propane-1,3-diyl)bis(oxy)]bis(methyle… · 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 5W8V · PDBe 5W8V · UniProt P00492
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