Research workbench

Adenylate kinase from sulfolobus acidocaldarius

Analyse Adenylate kinase from sulfolobus acidocaldarius in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1NKS
Type: protein
Length: 1,164 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Adenylate kinase
EC: 2.7.4.3
UniProt: P35028
Ligands: AMP, ADP
Pockets: 10 · best druggability 0.76

Structure

x-ray diffraction · 1 distinct chain · 51% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F	Adenylate kinase (EC 2.7.4.3)	protein	194	51% helix, 20% strand	P35028

Ligands and binding sites

AMP · Adenosine monophosphate · ligand · 3 copies · chains C, D, F
ADP · Adenosine-5'-diphosphate · ligand · chains F

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

Pockets

10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1031	0.76	0.78	82	empty
2	257	0.72	0.87	35	AMP
3	327	0.72	0.85	47	AMP, ADP
4	396	0.71	0.83	34	AMP
5	669	0.68	0.76	58	empty

Interfaces

9 interfaces between chains.

A–C · 834 Å² buried · 12 hydrogen bonds · protein-protein
D–E · 811 Å² buried · 8 hydrogen bonds · protein-protein
D–F · 807 Å² buried · 9 hydrogen bonds · protein-protein
A–B · 720 Å² buried · 7 hydrogen bonds · protein-protein
E–F · 719 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

1NKS · Adenylate kinase from sulfolobus acidocaldarius · the same entry in another collection · chain D against D, TM-score 1.00
P35028 · AlphaFold monomer V2.0 prediction for adenylate kinase (P35028) · 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 P35028
Elsewhere: RCSB PDB 1NKS · PDBe 1NKS · UniProt P35028

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