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Complex of substrate ADP-ribose with ibv NSP3 adrp domain

Analyse Complex of substrate ADP-ribose with ibv NSP3 adrp domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3EWP
Type: protein
Length: 345 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Non-structural protein 3
EC: 3.4.22.-
UniProt: P0C6V5
Ligands: APR
Pockets: 5 · best druggability 0.59

Structure

x-ray diffraction · 2 distinct chains · 39% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Non-structural protein 3 (EC 3.4.22.-)	protein	177	38% helix, 19% strand	P0C6V5
B	Non-structural protein 3 (EC 3.4.22.-)	protein	168	41% helix, 21% strand	P0C6V5

Ligands and binding sites

APR · Adenosine-5-diphosphoribose · ligand · 2 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	194	0.59	0.81	31	APR
2	173	0.59	0.82	31	APR
3	96	0.50	0.81	16	empty
4	154	0.46	0.77	27	empty
5	95	0.36	0.74	15	empty

Interfaces

1 interface between chains.

A–B · 668 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

3EWP · complex of substrate ADP-ribose with IBV Nsp3 ADRP domain · 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 P0C6V5
Elsewhere: RCSB PDB 3EWP · PDBe 3EWP · UniProt P0C6V5

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