Research workbench
Adenylate kinase from methanococcus voltae
Analyse Adenylate kinase from methanococcus voltae in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1KHT
- Type
- protein
- Length
- 572 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Adenylate kinase
- EC
- 2.7.4.3
- UniProt
- P43411
- Ligands
- AMP
- Pockets
- 4 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 51% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Adenylate kinase (EC 2.7.4.3) | protein | 190 | 51% helix, 17% strand | P43411 |
| B, C | Adenylate kinase (EC 2.7.4.3) | protein | 191 | 52% helix, 18% strand | P43411 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · 2 copies · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 527 | 0.75 | 0.83 | 59 | AMP |
| 2 | 406 | 0.73 | 0.84 | 53 | AMP |
| 3 | 362 | 0.58 | 0.76 | 37 | empty |
| 4 | 137 | 0.43 | 0.76 | 31 | empty |
Interfaces
3 interfaces between chains.
- A–C · 882 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 846 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 817 Ų buried · 10 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 P43411
- Elsewhere: RCSB PDB 1KHT · PDBe 1KHT · UniProt P43411
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