MolNFT v1 · #155915 · protein
Crystal structure of adenylate kinase from an extremophilic archaeon aeropyrum pernix with ATP and AMP
6LN3: “Crystal structure of adenylate kinase from an extremophilic archaeon aeropyrum pernix with ATP and AMP”. X-ray diffraction, 4 ligands (AMP, ATP, MG), 1 pocket (best druggability 0.73). MolNFT v1 #155915 on GenesisL1: 3D structure…
- PDB
- 6LN3
- Type
- protein
- Length
- 202 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Adenylate kinase
- EC
- 2.7.4.3
- UniProt
- Q9YDD2
- Ligands
- AMP, ATP, MG, CL
- Pockets
- 1 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 53% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Adenylate kinase (EC 2.7.4.3) | protein | 202 | 53% helix, 19% strand | Q9YDD2 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · chains A
- ATP · Adenosine-5'-triphosphate · ligand · chains A
- MG · Magnesium ion · metal · chains A
- CL · Chloride ion · ion · chains A
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 237 | 0.73 | 0.88 | 42 | AMP, ATP, MG |
Compared structures
- 6LN3 · Crystal structure of adenylate kinase from an extremophilic archaeon Aeropyrum pernix… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9YDD2 · AlphaFold monomer V2.0 prediction for adenylate kinase (Q9YDD2) · a predicted model of the same protein · chain A against A, TM-score 0.93
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 Q9YDD2
- Elsewhere: RCSB PDB 6LN3 · PDBe 6LN3 · UniProt Q9YDD2
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.