MolNFT v1 · #94746 · protein
Crystal structure of yeast AP4A phosphorylase APA2 in complex with AP4A
4I5V · 5',5'''-P-1,P-4-tetraphosphate phosphorylase 2: “Crystal structure of yeast AP4A phosphorylase APA2 in complex with AP4A”. X-ray diffraction, 1 ligand (B4P), 4 pockets (best druggability 0.76). MolNFT v1 #94746 on GenesisL1: 3D…
- PDB
- 4I5V
- Type
- protein
- Length
- 591 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
- B4P
- Pockets
- 4 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 22% 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 | 296 | 30% helix, 22% strand | P22108 |
| B | 5',5'''-P-1,P-4-tetraphosphate phosphorylase 2 (EC 2.7.7.53) | protein | 295 | 27% helix, 22% strand | P22108 |
Ligands and binding sites
- B4P · Bis(adenosine)-5'-tetraphosphate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 678 | 0.76 | 0.81 | 60 | B4P |
| 2 | 757 | 0.75 | 0.80 | 64 | B4P |
| 3 | 247 | 0.58 | 0.79 | 33 | empty |
| 4 | 228 | 0.57 | 0.79 | 35 | empty |
Interfaces
1 interface between chains.
- A–B · 531 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 4I5V · Crystal structure of yeast Ap4A phosphorylase Apa2 in complex with Ap4A · 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 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 P22108
- Elsewhere: RCSB PDB 4I5V · PDBe 4I5V · UniProt P22108
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