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High-resolution structures of adenylate kinase from yeast ligated with inhibitor AP5A, showing the pathway of phosphoryl transfer

Analyse High-resolution structures of adenylate kinase from yeast ligated with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1AKY
Type: protein
Length: 218 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Adenylate kinase
EC: 2.7.4.3
UniProt: P07170
Ligands: AP5
Pockets: 1 · best druggability 0.81

Structure

x-ray diffraction · 1 distinct chain · 50% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Adenylate kinase (EC 2.7.4.3)	protein	218	50% helix, 16% strand	P07170

Ligands and binding sites

AP5 · Bis(adenosine)-5'-pentaphosphate · ligand · chains A
IMD · Imidazole · 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.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	528	0.81	0.87	65	AP5, IMD

Compared structures

1AKY · High-resolution structures of adenylate kinase from yeast ligated with inhibitor AP5A… · the same entry in another collection · chain A against A, TM-score 1.00
P07170 · AlphaFold monomer V2.0 prediction for adenylate kinase (P07170) · 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 P07170
Elsewhere: RCSB PDB 1AKY · PDBe 1AKY · UniProt P07170

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