Research workbench
Crystal structure of yeast AP4A phosphorylase APA2 in complex with AMP
Analyse Crystal structure of yeast AP4A phosphorylase APA2 in complex with AMP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4I5W
- Type
- protein
- Length
- 574 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5',5'''-P-1,P-4-tetraphosphate phosphorylase 2
- EC
- 2.7.7.53
- UniProt
- P22108
- Ligands
- AMP, PO4
- Pockets
- 7 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 28% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 5',5'''-P-1,P-4-tetraphosphate phosphorylase 2 (EC 2.7.7.53) | protein | 292 | 28% helix, 22% strand | P22108 |
| B | 5',5'''-P-1,P-4-tetraphosphate phosphorylase 2 (EC 2.7.7.53) | protein | 282 | 28% helix, 23% strand | P22108 |
Ligands and binding sites
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 | 489 | 0.68 | 0.78 | 51 | AMP |
| 2 | 470 | 0.67 | 0.78 | 53 | AMP |
| 3 | 81 | 0.59 | 0.88 | 27 | empty |
| 4 | 325 | 0.56 | 0.76 | 41 | empty |
| 5 | 128 | 0.43 | 0.76 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 575 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 4I5W · Crystal structure of yeast Ap4A phosphorylase Apa2 in complex with AMP · the same entry in another collection · chain A against A, TM-score 1.00
- P22108 · AlphaFold monomer V2.0 prediction for diadenosine 5',5'''-P1,P4-tetraphosphate… · 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 P22108
- Elsewhere: RCSB PDB 4I5W · PDBe 4I5W · UniProt P22108
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