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Crystal structure of SARS-cov-2 nendou in complex with CSC000178569

Analyse Crystal structure of SARS-cov-2 nendou in complex with CSC000178569 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7N7W
Type: protein
Length: 696 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Uridylate-specific endoribonuclease
EC: 3.1.-.-
UniProt: P0DTD1
Ligands: 0OI
Pockets: 8 · best druggability 0.61

Structure

x-ray diffraction · 1 distinct chain · 22% helix, 31% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Uridylate-specific endoribonuclease (EC 3.1.-.-)	protein	348	22% helix, 31% strand	P0DTD1

Ligands and binding sites

0OI · N-(2-fluorophenyl)-N'-methylurea · ligand · chains B

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

Pockets

8 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	221	0.61	0.81	31	empty
2	231	0.60	0.80	28	empty
3	119	0.41	0.75	21	empty
4	124	0.39	0.74	21	empty
5	86	0.33	0.74	20	empty

Interfaces

1 interface between chains.

A–B · 589 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

7N7W · Crystal Structure of SARS-CoV-2 NendoU in complex with CSC000178569 · 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 P0DTD1
Elsewhere: RCSB PDB 7N7W · PDBe 7N7W · UniProt P0DTD1

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