Research workbench
Crystal structure of adenylate kinase variant AKLSE1
Analyse Crystal structure of adenylate kinase variant AKLSE1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3DKV
- Type
- protein
- Length
- 217 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Adenylate kinase
- EC
- 2.7.4.3
- UniProt
- P16304
- Ligands
- AP5, ZN, MG
- Pockets
- 2 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 53% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Adenylate kinase (EC 2.7.4.3) | protein | 217 | 53% helix, 17% strand | P16304 |
Ligands and binding sites
- AP5 · Bis(adenosine)-5'-pentaphosphate · ligand · chains A
- ZN · Zinc ion · metal · chains A
- MG · Magnesium ion · metal · chains A
- EDO · 1,2-ethanediol · additive · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 466 | 0.80 | 0.88 | 58 | MG, AP5, EDO |
| 2 | 63 | 0.53 | 0.87 | 21 | empty |
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 P16304
- Elsewhere: RCSB PDB 3DKV · PDBe 3DKV · UniProt P16304
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