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Crystal structure of adenylate kinase

Analyse Crystal structure of adenylate kinase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5XZ2
Type: protein
Length: 384 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Adenylate kinase isoenzyme 1
EC: 2.7.4.3, 2.7.4.6
UniProt: Q68EH2
Ligands: AP5, SO4
Pockets: 2 · best druggability 0.86

Structure

x-ray diffraction · 1 distinct chain · 61% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Adenylate kinase isoenzyme 1 (EC 2.7.4.3, 2.7.4.6)	protein	192	61% helix, 13% strand	Q68EH2

Ligands and binding sites

AP5 · Bis(adenosine)-5'-pentaphosphate · ligand · 2 copies · chains A, B
SO4 · Sulfate ion · ion · 2 copies · chains A, B

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.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	831	0.86	0.89	83	AP5
2	345	0.80	0.90	44	AP5

Interfaces

1 interface between chains.

A–B · 817 Å² buried · 9 hydrogen bonds · protein-protein

Compared structures

5XZ2 · Crystal structure of adenylate kinase · the same entry in another collection · chain A against A, TM-score 1.00

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 Q68EH2
Elsewhere: RCSB PDB 5XZ2 · PDBe 5XZ2 · UniProt Q68EH2

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