MolNFT v1 · #139150 · protein

Crystal structure of B. subtilis adenylate kinase variant

5X6I: “Crystal structure of B. subtilis adenylate kinase variant”. X-ray diffraction, 4 ligands (AP5, CA, ZN), 3 pockets (best druggability 0.80). MolNFT v1 #139150 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5X6I
Type: protein
Length: 212 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Adenylate kinase
EC: 2.7.4.3
UniProt: A0A063X902
Ligands: AP5, CA, ZN, MG
Pockets: 3 · best druggability 0.80

Structure

x-ray diffraction · 1 distinct chain · 51% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Adenylate kinase (EC 2.7.4.3)	protein	212	51% helix, 17% strand	A0A063X902

Ligands and binding sites

AP5 · Bis(adenosine)-5'-pentaphosphate · ligand · chains A
CA · Calcium ion · metal · 2 copies · chains A
ZN · Zinc ion · metal · chains A
MG · Magnesium ion · metal · chains A

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	525	0.80	0.86	62	MG, AP5
2	57	0.52	0.87	21	empty
3	58	0.32	0.77	12	empty

Compared structures

5X6I · Crystal structure of B. subtilis 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
Every structure of UniProt A0A063X902
Elsewhere: RCSB PDB 5X6I · PDBe 5X6I · UniProt A0A063X902

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