MolNFT v1 · #146250 · protein

Crystal structure of nudix 1 from arabidopsis thaliana

6DBY · Nudix hydrolase 1: “Crystal structure of nudix 1 from arabidopsis thaliana”. X-ray diffraction, 1 ligand (MG), 4 pockets (best druggability 0.73). MolNFT v1 #146250 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6DBY
Type: protein
Length: 277 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Nudix hydrolase 1
EC: 3.6.1.55, 3.6.1.67, 3.6.1.22
UniProt: Q9CA40
Ligands: MG
Pockets: 4 · best druggability 0.73

Structure

x-ray diffraction · 2 distinct chains · 15% helix, 41% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Nudix hydrolase 1 (EC 3.6.1.55, 3.6.1.67, 3.6.1.22)	protein	139	15% helix, 40% strand	Q9CA40
B	Nudix hydrolase 1 (EC 3.6.1.55, 3.6.1.67, 3.6.1.22)	protein	138	15% helix, 41% strand	Q9CA40

Ligands and binding sites

MG · Magnesium ion · metal · chains A

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

Pockets

4 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	268	0.73	0.86	38	empty
2	285	0.72	0.85	35	empty
3	122	0.41	0.75	21	empty
4	101	0.38	0.75	16	empty

Interfaces

1 interface between chains.

A–B · 955 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

6DBY · Crystal structure of Nudix 1 from Arabidopsis thaliana · the same entry in another collection · chain A against A, TM-score 1.00
Q9CA40 · AlphaFold monomer V2.0 prediction for nudix hydrolase 1 (Q9CA40) · 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 Q9CA40
Elsewhere: RCSB PDB 6DBY · PDBe 6DBY · UniProt Q9CA40

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