MolNFT v1 · #104475 · protein

Crystal structure of a stable adenylate kinase variant AKLSE4

4QBG: “Crystal structure of a stable adenylate kinase variant AKLSE4”. X-ray diffraction, 3 ligands (AP5, ZN, MG), 3 pockets (best druggability 0.75). MolNFT v1 #104475 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4QBG
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: P16304
Ligands: AP5, ZN, MG
Pockets: 3 · best druggability 0.75

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	Adenylate kinase (EC 2.7.4.3)	protein	217	48% helix, 17% strand	P16304

Ligands and binding sites

AP5 · Bis(adenosine)-5'-pentaphosphate · ligand · chains B
ZN · Zinc ion · metal · chains B
MG · Magnesium ion · metal · chains 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, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	477	0.75	0.84	48	AP5, MG
2	55	0.35	0.78	12	empty
3	75	0.30	0.73	12	empty

Compared structures

4QBG · Crystal structure of a stable adenylate kinase variant AKlse4 · the same entry in another collection · chain B against B, TM-score 1.00
P16304 · AlphaFold monomer V2.0 prediction for adenylate kinase (P16304) · a predicted model of the same protein · chain B against A, TM-score 0.90

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 P16304
Elsewhere: RCSB PDB 4QBG · PDBe 4QBG · UniProt P16304

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