Research workbench
Crystal structure of adenylate kinase of E. COLI with ADP/AMP bound
Analyse Crystal structure of adenylate kinase of E. COLI with ADP/AMP bound in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4JZK
- Type
- protein
- Length
- 428 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Adenylate kinase
- EC
- 2.7.4.3
- UniProt
- K0BFA4
- Ligands
- ADP, AMP
- Pockets
- 6 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 48% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Adenylate kinase (EC 2.7.4.3) | protein | 214 | 48% helix, 18% strand | K0BFA4 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- AMP · Adenosine monophosphate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 395 | 0.82 | 0.91 | 59 | ADP, AMP |
| 2 | 446 | 0.81 | 0.89 | 66 | ADP, AMP |
| 3 | 138 | 0.47 | 0.78 | 15 | empty |
| 4 | 53 | 0.44 | 0.83 | 12 | empty |
| 5 | 80 | 0.36 | 0.76 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 403 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 4JZK · Crystal Structure of Adenylate kinase of E. Coli with ADP/AMP bound · the same entry in another collection · chain A 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 K0BFA4
- Elsewhere: RCSB PDB 4JZK · PDBe 4JZK · UniProt K0BFA4
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