Research workbench
Crystal structure of E. coli Adenylate kinase G56C/T163C double mutant in complex with Ap5a
Analyse Crystal structure of E. coli Adenylate kinase G56C/T163C double mutant in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5EJE
- Type
- protein
- Length
- 428 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.9
- Source
- Escherichia coli
- Molecule
- Adenylate kinase
- EC
- 2.7.4.3
- UniProt
- A7ZIN4
- Ligands
- AP5, CO
- Pockets
- 5 · best druggability 0.82
Structure
x-ray diffraction · resolution 1.9 · 1 distinct chain · 47% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Adenylate kinase (EC 2.7.4.3) | protein | 214 | 47% helix, 17% strand | A7ZIN4 |
Ligands and binding sites
- AP5 · Bis(adenosine)-5'-pentaphosphate · ligand · 2 copies · chains A, B
- CO · Cobalt (II) ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 520 | 0.82 | 0.88 | 67 | AP5, CO |
| 2 | 589 | 0.81 | 0.86 | 83 | AP5, CO |
| 3 | 120 | 0.43 | 0.77 | 18 | empty |
| 4 | 69 | 0.37 | 0.77 | 14 | empty |
| 5 | 72 | 0.36 | 0.77 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 382 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5EJE · Crystal structure of E. COLI adenylate kinase G56C/T163C double mutant in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
- A7ZIN4 · AlphaFold monomer V2.0 prediction for adenylate kinase (A7ZIN4) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 A7ZIN4
- Elsewhere: RCSB PDB 5EJE · PDBe 5EJE · UniProt A7ZIN4
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