Research workbench
Crystal structure of AMP phosphorylase N-terminal deletion mutant
Analyse Crystal structure of AMP phosphorylase N-terminal deletion mutant in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4GA4
- Type
- protein
- Length
- 836 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative thymidine phosphorylase
- EC
- 2.4.2.4
- UniProt
- Q5JCX3
- Ligands
- PO4
- Pockets
- 7 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 49% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Putative thymidine phosphorylase (EC 2.4.2.4) | protein | 418 | 49% helix, 16% strand | Q5JCX3 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
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 | 667 | 0.74 | 0.80 | 78 | PO4 |
| 2 | 663 | 0.71 | 0.78 | 64 | PO4 |
| 3 | 539 | 0.68 | 0.78 | 77 | empty |
| 4 | 258 | 0.55 | 0.77 | 48 | empty |
| 5 | 51 | 0.48 | 0.86 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1060 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
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 Q5JCX3
- Elsewhere: RCSB PDB 4GA4 · PDBe 4GA4 · UniProt Q5JCX3
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