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The crystal structure of nudix hydrolase from rhodospirillum rubrum

Analyse The crystal structure of nudix hydrolase from rhodospirillum rubrum in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3R03
Type: protein
Length: 260 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Nudix hydrolase
UniProt: Q2RXE7
Ligands: ADP
Pockets: 3 · best druggability 0.56

Structure

x-ray diffraction · 2 distinct chains · 23% helix, 34% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Nudix hydrolase	protein	131	23% helix, 34% strand	Q2RXE7
B	Nudix hydrolase	protein	129	23% helix, 34% strand	Q2RXE7

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · ligand · chains A

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

Pockets

3 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	225	0.56	0.79	28	ADP
2	199	0.52	0.77	26	empty
3	76	0.36	0.76	11	empty

Interfaces

1 interface between chains.

A–B · 744 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 modified (engineered).

Compared structures

3R03 · The crystal structure of NUDIX hydrolase from Rhodospirillum rubrum · the same entry in another collection · chain B against B, 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 Q2RXE7
Elsewhere: RCSB PDB 3R03 · PDBe 3R03 · UniProt Q2RXE7

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