Research workbench
Crystal structure of a stable adenylate kinase variant AKLSE5
Analyse Crystal structure of a stable adenylate kinase variant AKLSE5 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4QBH
- Type
- protein
- Length
- 432 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Adenylate kinase
- EC
- 2.7.4.3
- UniProt
- P27142
- Ligands
- AP5, ZN, MG
- Pockets
- 5 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 51% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Adenylate kinase (EC 2.7.4.3) | protein | 217 | 51% helix, 17% strand | P27142 |
| B | Adenylate kinase (EC 2.7.4.3) | protein | 215 | 52% helix, 17% strand | P27142 |
Ligands and binding sites
- AP5 · Bis(adenosine)-5'-pentaphosphate · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- MG · Magnesium 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 382 | 0.80 | 0.90 | 53 | AP5, MG |
| 2 | 475 | 0.79 | 0.87 | 63 | AP5, MG |
| 3 | 137 | 0.59 | 0.84 | 26 | empty |
| 4 | 249 | 0.55 | 0.77 | 33 | empty |
| 5 | 150 | 0.48 | 0.78 | 29 | empty |
Interfaces
1 interface between chains.
- A–B · 769 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
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 P27142
- Elsewhere: RCSB PDB 4QBH · PDBe 4QBH · UniProt P27142
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.