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Crystal structure of the nudix hydrolase DR1025 in complex with ATP

Analyse Crystal structure of the nudix hydrolase DR1025 in complex with ATP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1SU2
Type: protein
Length: 318 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: MUTT/NUDIX family protein
UniProt: Q9RVK2
Ligands: ATP, MG
Pockets: 5 · best druggability 0.54

Structure

x-ray diffraction · 1 distinct chain · 22% helix, 34% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	MUTT/NUDIX family protein	protein	159	22% helix, 34% strand	Q9RVK2

Ligands and binding sites

ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, B
MG · Magnesium ion · metal · 6 copies · chains A, B

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

Pockets

5 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	215	0.54	0.78	27	empty
2	190	0.49	0.76	27	empty
3	58	0.34	0.78	17	empty
4	64	0.33	0.76	16	empty
5	79	0.30	0.73	17	MG, ATP

Interfaces

1 interface between chains.

A–B · 1861 Å² buried · 26 hydrogen bonds · protein-protein

Compared structures

1SU2 · Crystal structure of the nudix hydrolase DR1025 in complex with ATP · the same entry in another collection · chain A against A, TM-score 1.00

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 Q9RVK2
Elsewhere: RCSB PDB 1SU2 · PDBe 1SU2 · UniProt Q9RVK2

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