MolNFT v1 · #104477 · protein

Crystal structure of a stable adenylate kinase variant AKLSE6

4QBI: “Crystal structure of a stable adenylate kinase variant AKLSE6”. X-ray diffraction, 3 ligands (AP5, ZN, MG), 6 pockets (best druggability 0.83). MolNFT v1 #104477 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4QBI
Type: protein
Length: 431 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Adenylate kinase
EC: 2.7.4.3
UniProt: P27142
Ligands: AP5, ZN, MG
Pockets: 6 · best druggability 0.83

Structure

x-ray diffraction · 2 distinct chains · 50% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Adenylate kinase (EC 2.7.4.3)	protein	217	51% helix, 16% strand	P27142
B	Adenylate kinase (EC 2.7.4.3)	protein	214	50% helix, 16% strand	P27142

Ligands and binding sites

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

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	500	0.83	0.89	64	MG, AP5
2	609	0.81	0.86	67	MG, AP5
3	124	0.59	0.85	28	empty
4	189	0.53	0.78	29	empty
5	225	0.51	0.76	26	empty

Interfaces

1 interface between chains.

A–B · 700 Å² buried · 17 hydrogen bonds · protein-protein

Compared structures

4QBI · Crystal structure of a stable adenylate kinase variant AKlse6 · the same entry in another collection · chain A against A, TM-score 1.00
P27142 · AlphaFold monomer V2.0 prediction for adenylate kinase (P27142) · 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 P27142
Elsewhere: RCSB PDB 4QBI · PDBe 4QBI · UniProt P27142

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