MolNFT v1 · #74530 · protein
Crystal structure of plasmodium falciparum hypoxanthine-guanine- xanthine phosphoribosyltransferase in complex with S-serme-immh phosphonate
3OZG · Hypoxanthine-guanine-xanthine phosphoribosyltransferase: “Crystal structure of plasmodium falciparum hypoxanthine-guanine- xanthine phosphoribosyltransferase in…”. X-ray diffraction, 3 ligands (SSI, POP, MG), 16 pockets (best…
- PDB
- 3OZG
- Type
- protein
- Length
- 913 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hypoxanthine-guanine-xanthine phosphoribosyltransferase
- EC
- 2.4.2.-
- UniProt
- P20035
- Ligands
- SSI, POP, MG
- Pockets
- 16 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 29% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hypoxanthine-guanine-xanthine phosphoribosyltransferase (EC 2.4.2.-) | protein | 227 | 30% helix, 33% strand | P20035 |
| B, D | Hypoxanthine-guanine-xanthine phosphoribosyltransferase (EC 2.4.2.-) | protein | 228 | 27% helix, 32% strand | P20035 |
| C | Hypoxanthine-guanine-xanthine phosphoribosyltransferase (EC 2.4.2.-) | protein | 230 | 29% helix, 32% strand | P20035 |
Ligands and binding sites
- SSI · [(3S)-4-hydroxy-3-{[(4-oxo-4,5-dihydro-3H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]amino}butyl]phosphonic acid · ligand · 4 copies · chains A, B, C, D
- POP · Pyrophosphate 2- · 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
16 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 231 | 0.81 | 0.94 | 34 | SSI, POP, MG |
| 2 | 224 | 0.80 | 0.93 | 34 | MG, SSI, POP |
| 3 | 221 | 0.80 | 0.93 | 32 | SSI, POP, MG |
| 4 | 221 | 0.79 | 0.93 | 33 | SSI, POP, MG |
| 5 | 549 | 0.75 | 0.83 | 52 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1458 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 816 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 3OZG · Crystal Structure of Plasmodium falciparum Hypoxanthine-Guanine-Xanthine… · the same entry in another collection · chain A against A, TM-score 1.00
- P20035 · AlphaFold monomer V2.0 prediction for hypoxanthine-guanine-xanthine… · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P20035
- Elsewhere: RCSB PDB 3OZG · PDBe 3OZG · UniProt P20035
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