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Crystal structure of human NUDT5 complexed with 8-oxo-dgdp and manganese

Analyse Crystal structure of human NUDT5 complexed with 8-oxo-dgdp and manganese in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3AC9
Type: protein
Length: 390 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: ADP-sugar pyrophosphatase
EC: 3.6.1.13
UniProt: Q9UKK9
Ligands: 8GD, MN
Pockets: 3 · best druggability 0.72

Structure

x-ray diffraction · 1 distinct chain · 23% helix, 43% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	ADP-sugar pyrophosphatase (EC 3.6.1.13)	protein	195	23% helix, 43% strand	Q9UKK9

Ligands and binding sites

8GD · 2'-deoxy-8-oxoguanosine 5'-(trihydrogen diphosphate) · ligand · 2 copies · chains A, B
MN · Manganese (II) ion · metal · 2 copies · chains B

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	368	0.72	0.83	43	8GD
2	383	0.71	0.83	42	8GD, MN
3	52	0.24	0.73	18	empty

Interfaces

1 interface between chains.

A–B · 3186 Å² buried · 29 hydrogen bonds · protein-protein

Compared structures

3AC9 · Crystal structure of human NUDT5 complexed with 8-oxo-dGDP and manganese · 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 Q9UKK9
Elsewhere: RCSB PDB 3AC9 · PDBe 3AC9 · UniProt Q9UKK9

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