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Crystal structure of poecilia reticulata adenylate kinase

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

PDB: 5YCD
Type: protein
Length: 384 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Adenylayte kinase
Ligands: AP5, MG
Pockets: 2 · best druggability 0.82

Structure

x-ray diffraction · 2 distinct chains · 58% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Adenylayte kinase	protein	191	57% helix, 13% strand	—
B	Adenylayte kinase	protein	193	59% helix, 13% strand	—

Ligands and binding sites

AP5 · Bis(adenosine)-5'-pentaphosphate · ligand · 2 copies · chains A, B
MG · Magnesium ion · metal · 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	594	0.82	0.87	64	AP5, MG
2	519	0.80	0.87	64	AP5, MG

Interfaces

1 interface between chains.

A–B · 675 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

5YCD · Crystal structure of Poecilia reticulata 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
Elsewhere: RCSB PDB 5YCD · PDBe 5YCD

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