Research workbench
Crystal structure of AMP phosphorylase C-terminal deletion mutant in the apo-form
Analyse Crystal structure of AMP phosphorylase C-terminal deletion mutant in the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4GA5
- Type
- protein
- Length
- 3,944 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.25
- Source
- Thermococcus kodakarensis
- Molecule
- Putative thymidine phosphorylase
- EC
- 2.4.2.4
- UniProt
- Q5JCX3
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · resolution 3.25 · 1 distinct chain · 44% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, A, C, D, E, F, G, H | Putative thymidine phosphorylase (EC 2.4.2.4) | protein | 493 | 44% helix, 20% strand | Q5JCX3 |
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 902 | 0.79 | 0.81 | 86 | empty |
| 2 | 671 | 0.76 | 0.82 | 64 | empty |
| 3 | 764 | 0.75 | 0.80 | 82 | empty |
| 4 | 770 | 0.74 | 0.79 | 62 | empty |
| 5 | 698 | 0.73 | 0.79 | 63 | empty |
Interfaces
13 interfaces between chains.
- D–H · 1665 Ų buried · 13 hydrogen bonds · protein-protein
- C–G · 1646 Ų buried · 13 hydrogen bonds · protein-protein
- B–F · 1643 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 302 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 287 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4GA5 · Crystal structure of AMP phosphorylase C-terminal deletion mutant in the apo-form · the same entry in another collection · chain H against H, TM-score 1.00
- Q5JCX3 · AlphaFold monomer V2.0 prediction for AMP phosphorylase (Q5JCX3) · a predicted model of the same protein · chain G 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 Q5JCX3
- Elsewhere: RCSB PDB 4GA5 · PDBe 4GA5 · UniProt Q5JCX3
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