MolNFT v1 · #95220 · protein
Human hypoxanthine-guanine phosphoribosyltransferase in complex with [(2-((guanine-9H-YL)METHYL)PROPANE-1,3-DIYL)BIS(OXY)]BIS(METHYLENE)) diphosphonic acid
4IJQ: “Human hypoxanthine-guanine phosphoribosyltransferase in complex with…”. X-ray diffraction, 3 ligands (SV2, MG, SO4), 13 pockets (best druggability 0.83). MolNFT v1 #95220 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4IJQ
- Type
- protein
- Length
- 810 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
- SV2, MG, SO4
- Pockets
- 13 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 31% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hypoxanthine-guanine phosphoribosyltransferase (EC 2.4.2.8) | protein | 198 | 32% helix, 29% strand | P00492 |
| B | Hypoxanthine-guanine phosphoribosyltransferase (EC 2.4.2.8) | protein | 203 | 31% helix, 30% 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
- SV2 · [{2-[(guanine-9-yl)methyl]propane-1,3-diyl}bis(oxymethylene)]bis(phosphonic acid) · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 8 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1078 | 0.83 | 0.84 | 76 | empty |
| 2 | 274 | 0.58 | 0.78 | 26 | SV2, SO4, MG |
| 3 | 198 | 0.55 | 0.78 | 33 | empty |
| 4 | 167 | 0.54 | 0.79 | 34 | empty |
| 5 | 225 | 0.51 | 0.76 | 25 | SV2, MG, SO4 |
Interfaces
6 interfaces between chains.
- B–D · 1677 Ų buried · 26 hydrogen bonds · protein-protein
- A–C · 1654 Ų buried · 28 hydrogen bonds · protein-protein
- C–D · 864 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 861 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 364 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 4IJQ · Human hypoxanthine-guanine phosphoribosyltransferase in complex with… · the same entry in another collection · chain D against D, TM-score 1.00
- P00492 · AlphaFold monomer V2.0 prediction for hypoxanthine-guanine phosphoribosyltransferase… · a predicted model of the same protein · chain B against A, TM-score 0.99
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 4IJQ · PDBe 4IJQ · UniProt P00492
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