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Crystal structure of notothenia coriiceps adenylate kinase variant

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

PDB: 5YCB
Type: protein
Length: 375 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Adenylate kinase
Ligands: AP5, SO4
Pockets: 3 · best druggability 0.74

Structure

x-ray diffraction · 2 distinct chains · 59% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Adenylate kinase	protein	189	58% helix, 14% strand	—
B	Adenylate kinase	protein	186	60% helix, 15% strand	—

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

3 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	326	0.74	0.86	45	AP5
2	325	0.74	0.86	42	AP5
3	113	0.35	0.72	18	empty

Interfaces

1 interface between chains.

A–B · 302 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

5YCB · Crystal structure of notothenia coriiceps adenylate kinase variant · 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 5YCB · PDBe 5YCB

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