MolNFT v1 · #75912 · protein

Crystal structure of cdp-chase in complex with GD3+

3Q4I · Phosphohydrolase (MUTT/NUDIX family protein): “Crystal structure of cdp-chase in complex with GD3+”. X-ray diffraction, 1 ligand (GD3), 5 pockets (best druggability 0.72). MolNFT v1 #75912 on GenesisL1: 3D structure, binding sites…

PDB: 3Q4I
Type: protein
Length: 408 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Phosphohydrolase (MUTT/NUDIX family protein)
UniProt: Q81EE8
Ligands: GD3
Pockets: 5 · best druggability 0.72

Structure

x-ray diffraction · 1 distinct chain · 38% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Phosphohydrolase (MUTT/NUDIX family protein)	protein	204	38% helix, 26% strand	Q81EE8

Ligands and binding sites

GD3 · Gadolinium ion · metal · 3 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, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	462	0.72	0.82	47	GD3
2	372	0.65	0.79	57	GD3
3	84	0.38	0.77	14	empty
4	70	0.31	0.74	20	empty
5	60	0.28	0.74	14	empty

Interfaces

1 interface between chains.

A–B · 3300 Å² buried · 30 hydrogen bonds · protein-protein

Compared structures

3Q4I · Crystal structure of CDP-Chase in complex with Gd3+ · 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 Q81EE8
Elsewhere: RCSB PDB 3Q4I · PDBe 3Q4I · UniProt Q81EE8

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