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Apo-dutpase from arabidopsis thaliana

Analyse Apo-dutpase from arabidopsis thaliana in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4OOQ
Type: protein
Length: 388 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Deoxyuridine 5'-triphosphate nucleotidohydrolase
EC: 3.6.1.23
UniProt: Q9STG6
Ligands: MG, SO4
Pockets: 4 · best druggability 0.79

Structure

x-ray diffraction · 3 distinct chains · 5% helix, 46% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Deoxyuridine 5'-triphosphate nucleotidohydrolase (EC 3.6.1.23)	protein	131	5% helix, 46% strand	Q9STG6
B	Deoxyuridine 5'-triphosphate nucleotidohydrolase (EC 3.6.1.23)	protein	130	5% helix, 46% strand	Q9STG6
C	Deoxyuridine 5'-triphosphate nucleotidohydrolase (EC 3.6.1.23)	protein	127	6% helix, 45% strand	Q9STG6

Ligands and binding sites

MG · Magnesium ion · metal · chains A, B, C
SO4 · Sulfate ion · ion · 2 copies · chains A, B, C

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

Pockets

4 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	133	0.79	0.97	27	empty
2	180	0.48	0.76	27	empty
3	159	0.45	0.76	26	empty
4	103	0.38	0.75	23	empty

Interfaces

3 interfaces between chains.

A–B · 1768 Å² buried · 26 hydrogen bonds · protein-protein
A–C · 1698 Å² buried · 23 hydrogen bonds · protein-protein
B–C · 1683 Å² buried · 27 hydrogen bonds · protein-protein

Compared structures

4OOQ · apo-dUTPase from Arabidopsis thaliana · the same entry in another collection · chain C against C, TM-score 1.00
Q9STG6 · AlphaFold monomer V2.0 prediction for deoxyuridine 5'-triphosphate nucleotidohydrolase… · a predicted model of the same protein · chain C 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 Q9STG6
Elsewhere: RCSB PDB 4OOQ · PDBe 4OOQ · UniProt Q9STG6

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