MolNFT v1 · #96489 · protein

A high resolution structure of aquifex adenylate kinase with 2 ADP'S

4JL5: “A high resolution structure of aquifex adenylate kinase with 2 ADP'S”. X-ray diffraction, 1 ligand (ADP), 2 pockets (best druggability 0.79). MolNFT v1 #96489 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4JL5
Type: protein
Length: 406 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Adenylate kinase
EC: 2.7.4.3
UniProt: O66490
Ligands: ADP
Pockets: 2 · best druggability 0.79

Structure

x-ray diffraction · 1 distinct chain · 52% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Adenylate kinase (EC 2.7.4.3)	protein	203	52% helix, 16% strand	O66490

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · ligand · 4 copies · chains A, B

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

Pockets

2 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	949	0.79	0.81	92	ADP
2	584	0.79	0.85	67	ADP

Interfaces

1 interface between chains.

A–B · 334 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

4JL5 · A high resolution structure of Aquifex Adenylate kinase with 2 ADP's · the same entry in another collection · chain A against A, TM-score 1.00
O66490 · AlphaFold monomer V2.0 prediction for adenylate kinase (O66490) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 O66490
Elsewhere: RCSB PDB 4JL5 · PDBe 4JL5 · UniProt O66490

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