Research workbench

Crystal structure of xiphophorus maculatus adenylate kinase

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

PDB: 5YCF
Type: protein
Length: 377 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: M4AA20
Ligands: AP5
Pockets: 2 · best druggability 0.79

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	Adenylate kinase isoenzyme 1 (EC 2.7.4.3, 2.7.4.6)	protein	188	60% helix, 13% strand	M4AA20
A	Adenylate kinase isoenzyme 1 (EC 2.7.4.3, 2.7.4.6)	protein	189	57% helix, 13% strand	M4AA20

Ligands and binding sites

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

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	858	0.79	0.82	70	AP5
2	488	0.76	0.84	60	AP5

Interfaces

1 interface between chains.

B–A · 307 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

5YCF · Crystal structure of Xiphophorus maculatus adenylate kinase · the same entry in another collection · chain B against B, 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 M4AA20
Elsewhere: RCSB PDB 5YCF · PDBe 5YCF · UniProt M4AA20

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.