Research workbench

Crystal structure of adenylate kinase from burkholderia pseudomallei

Analyse Crystal structure of adenylate kinase from burkholderia pseudomallei in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3GMT
Type: protein
Length: 403 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Adenylate kinase
EC: 2.7.4.3
UniProt: Q3JVB1
Ligands: SO4
Pockets: 3 · best druggability 0.49

Structure

x-ray diffraction · 2 distinct chains · 48% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Adenylate kinase (EC 2.7.4.3)	protein	204	48% helix, 17% strand	Q3JVB1
B	Adenylate kinase (EC 2.7.4.3)	protein	199	48% helix, 16% strand	Q3JVB1

Ligands and binding sites

SO4 · Sulfate ion · ion · 4 copies · chains A, 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, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	172	0.49	0.77	25	SO4
2	109	0.45	0.79	14	empty
3	95	0.36	0.75	25	SO4

Interfaces

1 interface between chains.

A–B · 561 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 10 modified (engineered).

Compared structures

3GMT · Crystal structure of adenylate kinase from burkholderia pseudomallei · the same entry in another collection · chain A against A, TM-score 1.00
Q3JVB1 · AlphaFold monomer V2.0 prediction for adenylate kinase (Q3JVB1) · a predicted model of the same protein · chain A against A, TM-score 0.62

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 Q3JVB1
Elsewhere: RCSB PDB 3GMT · PDBe 3GMT · UniProt Q3JVB1

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.