MolNFT v1 · #137282 · protein
Crystal structure of adenine phosphoribosyltransferase from saccharomyces cerevisiae complexed with L-2,5-dideoxy-2,5-imino- altritol 1,6-bisphosphate (L-diab) and adenine
5VJP · Adenine phosphoribosyltransferase 1: “Crystal structure of adenine phosphoribosyltransferase from saccharomyces cerevisiae complexed with…”. X-ray diffraction, 2 ligands (IR9, ADE), 2 pockets (best druggability 0.64). MolNFT v1…
- PDB
- 5VJP
- Type
- protein
- Length
- 351 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Adenine phosphoribosyltransferase 1
- EC
- 2.4.2.7
- UniProt
- P49435
- Ligands
- IR9, ADE
- Pockets
- 2 · best druggability 0.64
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Adenine phosphoribosyltransferase 1 (EC 2.4.2.7) | protein | 172 | 38% helix, 30% strand | P49435 |
| B | Adenine phosphoribosyltransferase 1 (EC 2.4.2.7) | protein | 179 | 37% helix, 32% strand | P49435 |
Ligands and binding sites
- IR9 · [(2S,3R,4S,5S)-3,4-dihydroxypyrrolidine-2,5-diyl]bis(methylene) bis[dihydrogen (phosphate)] · ligand · 2 copies · chains A, B
- ADE · Adenine · ligand · chains B
- EDO · 1,2-ethanediol · additive · 7 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 386 | 0.64 | 0.78 | 33 | IR9, ADE |
| 2 | 182 | 0.49 | 0.76 | 27 | IR9 |
Interfaces
1 interface between chains.
- A–B · 1599 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 5VJP · Crystal Structure of Adenine Phosphoribosyltransferase from Saccharomyces cerevisiae… · the same entry in another collection · chain A against A, TM-score 1.00
- P49435 · AlphaFold monomer V2.0 prediction for adenine phosphoribosyltransferase 1 (P49435) · a predicted model of the same protein · chain A 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 P49435
- Elsewhere: RCSB PDB 5VJP · PDBe 5VJP · UniProt P49435
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