Research workbench
Crystal structure of V148G adenylate kinase from E. COLI, in complex with AP5A
Analyse Crystal structure of V148G adenylate kinase from E. COLI, in complex with AP5A in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3HPR
- 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
- P69441
- Ligands
- AP5
- Pockets
- 4 · best druggability 0.83
Structure
x-ray diffraction · 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 | P69441 |
Ligands and binding sites
- AP5 · Bis(adenosine)-5'-pentaphosphate · ligand · 2 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 528 | 0.83 | 0.89 | 63 | AP5 |
| 2 | 518 | 0.81 | 0.88 | 70 | AP5 |
| 3 | 188 | 0.47 | 0.75 | 21 | empty |
| 4 | 63 | 0.35 | 0.78 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 371 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 3HPR · Crystal structure of V148G adenylate kinase from E. coli, in complex with Ap5A · the same entry in another collection · chain A against A, TM-score 1.00
- P69441 · AlphaFold monomer V2.0 prediction for adenylate kinase (P69441) · 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 P69441
- Elsewhere: RCSB PDB 3HPR · PDBe 3HPR · UniProt P69441
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