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Crystal structure of vaccinia virus decapping enzyme D9 in complex with trinucleotide substrate

Analyse Crystal structure of vaccinia virus decapping enzyme D9 in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7SF0
Type: protein
Length: 209 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA repair ntp-phosphohydrolase
UniProt: L7QJE0
Ligands: 8NK, MG, NA
Pockets: 3 · best druggability 0.69

Structure

x-ray diffraction · 1 distinct chain · 25% helix, 31% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA repair ntp-phosphohydrolase	protein	209	25% helix, 31% strand	L7QJE0

Ligands and binding sites

8NK · 7-methylguanosine 5'-diphosphate · ligand · chains A
MG · Magnesium ion · metal · 2 copies · chains A
NA · Sodium ion · metal · chains A

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

Pockets

3 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	319	0.69	0.83	35	8NK, MG
2	58	0.35	0.79	17	empty
3	59	0.31	0.75	14	empty

Compared structures

7SF0 · Crystal structure of Vaccinia Virus decapping enzyme D9 in complex with trinucleotide… · 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 L7QJE0
Elsewhere: RCSB PDB 7SF0 · PDBe 7SF0 · UniProt L7QJE0

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