MolNFT v1 · #21227 · protein

Crystal structure of adenylate kinase from bacillus globisporus

1S3G: “Crystal structure of adenylate kinase from bacillus globisporus”. X-ray diffraction, 2 ligands (AP5, ZN), 3 pockets (best druggability 0.80). MolNFT v1 #21227 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1S3G
Type: protein
Length: 217 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Adenylate kinase
EC: 2.7.4.3
UniProt: P84139
Ligands: AP5, ZN
Pockets: 3 · best druggability 0.80

Structure

x-ray diffraction · 1 distinct chain · 48% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Adenylate kinase (EC 2.7.4.3)	protein	217	48% helix, 17% strand	P84139

Ligands and binding sites

AP5 · Bis(adenosine)-5'-pentaphosphate · ligand · chains A
ZN · Zinc 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	528	0.80	0.87	60	AP5
2	72	0.56	0.87	23	empty
3	64	0.34	0.76	9	empty

Compared structures

1S3G · Crystal structure of adenylate kinase from Bacillus globisporus · the same entry in another collection · chain A against A, TM-score 1.00
P84139 · AlphaFold monomer V2.0 prediction for adenylate kinase (P84139) · a predicted model of the same protein · chain A against A, TM-score 0.98

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 P84139
Elsewhere: RCSB PDB 1S3G · PDBe 1S3G · UniProt P84139

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