Research workbench
Crystal structure of adenine phosphoribosyltransferase from saccharomyces cerevisiae complexed with D-2,5-dideoxy-2,5-imino- altritol 1,6-bisphosphate (D-diab) and adenine
Analyse Crystal structure of adenine phosphoribosyltransferase from saccharomyces… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5VJN
- Type
- protein
- Length
- 345 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
- IR8, ADE
- Pockets
- 1 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Adenine phosphoribosyltransferase 1 (EC 2.4.2.7) | protein | 176 | 36% helix, 33% strand | P49435 |
| B | Adenine phosphoribosyltransferase 1 (EC 2.4.2.7) | protein | 169 | 37% helix, 30% strand | P49435 |
Ligands and binding sites
- IR8 · [(2R,3S,4R,5R)-3,4-dihydroxypyrrolidine-2,5-diyl]bis(methylene) bis[dihydrogen (phosphate)] · ligand · 2 copies · chains A, B
- ADE · Adenine · ligand · chains A
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 612 | 0.68 | 0.77 | 70 | IR8, ADE |
Interfaces
1 interface between chains.
- A–B · 1589 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 5VJN · 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 B 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 P49435
- Elsewhere: RCSB PDB 5VJN · PDBe 5VJN · UniProt P49435
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