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Crystal structure of the N-terminal domain of human NUDT6

Analyse Crystal structure of the N-terminal domain of human NUDT6 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3FXT
Type: protein
Length: 711 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Nucleoside diphosphate-linked moiety X motif 6
UniProt: P53370
Pockets: 5 · best druggability 0.67

Structure

x-ray diffraction · 5 distinct chains · 37% helix, 30% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, F	Nucleoside diphosphate-linked moiety X motif 6	protein	90	37% helix, 31% strand	P53370
B	Nucleoside diphosphate-linked moiety X motif 6	protein	89	36% helix, 31% strand	P53370
D, G	Nucleoside diphosphate-linked moiety X motif 6	protein	88	38% helix, 30% strand	P53370
E	Nucleoside diphosphate-linked moiety X motif 6	protein	89	36% helix, 29% strand	P53370
H	Nucleoside diphosphate-linked moiety X motif 6	protein	87	37% helix, 30% strand	P53370

Ligands and binding sites

GOL · Glycerol · additive · 6 copies · chains B, C, A, D, E, F

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	662	0.67	0.76	69	GOL
2	159	0.50	0.78	25	empty
3	228	0.49	0.74	21	empty
4	202	0.43	0.73	32	empty
5	54	0.30	0.76	13	empty

Interfaces

8 interfaces between chains.

B–G · 640 Å² buried · 3 hydrogen bonds · protein-protein
A–E · 633 Å² buried · 3 hydrogen bonds · protein-protein
D–H · 611 Å² buried · 2 hydrogen bonds · protein-protein
A–F · 543 Å² buried · 10 hydrogen bonds · protein-protein
B–F · 493 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

3FXT · Crystal structure of the N-terminal domain of human NUDT6 · the same entry in another collection · chain H against H, TM-score 1.00
P53370 · AlphaFold monomer V2.0 prediction for nucleoside diphosphate-linked moiety X motif 6… · a predicted model of the same protein · chain D against A, TM-score 0.93

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 P53370
Elsewhere: RCSB PDB 3FXT · PDBe 3FXT · UniProt P53370

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