MolNFT v1 · #92507 · protein
Crystal structure of AMP phosphorylase C-terminal deletion mutant in complex with substrates
4GA6 · Putative thymidine phosphorylase: “Crystal structure of AMP phosphorylase C-terminal deletion mutant in complex with substrates”. X-ray diffraction, 2 ligands (AMP, SO4), 4 pockets (best druggability 0.88). MolNFT v1 #92507 on…
- PDB
- 4GA6
- Type
- protein
- Length
- 986 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
- AMP, SO4
- Pockets
- 4 · best druggability 0.88
Structure
x-ray diffraction · 1 distinct chain · 43% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Putative thymidine phosphorylase (EC 2.4.2.4) | protein | 493 | 43% helix, 21% strand | Q5JCX3 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 4 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 | 961 | 0.88 | 0.89 | 130 | AMP, SO4 |
| 2 | 196 | 0.80 | 0.94 | 45 | AMP, SO4 |
| 3 | 184 | 0.58 | 0.81 | 31 | empty |
| 4 | 116 | 0.55 | 0.83 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 1775 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 4GA6 · Crystal structure of AMP phosphorylase C-terminal deletion mutant in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
- Q5JCX3 · AlphaFold monomer V2.0 prediction for AMP phosphorylase (Q5JCX3) · a predicted model of the same protein · chain B against A, TM-score 0.92
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 4GA6 · PDBe 4GA6 · UniProt Q5JCX3
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