MolNFT v1 · #133810 · protein

Pandda analysis group deposition of ground-state model of SARS-cov-2 nendou

5SBF · Uridylate-specific endoribonuclease: “Pandda analysis group deposition of ground-state model of SARS-cov-2 nendou”. X-ray diffraction, 8 pockets (best druggability 0.60). MolNFT v1 #133810 on GenesisL1: 3D structure, binding sites…

PDB: 5SBF
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
Pockets: 8 · best druggability 0.60

Structure

x-ray diffraction · 1 distinct chain · 21% helix, 32% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Uridylate-specific endoribonuclease (EC 3.1.-.-)	protein	348	21% helix, 32% strand	P0DTD1

Ligands and binding sites

CIT · Citric acid · additive · 2 copies · chains A, 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	265	0.60	0.79	33	empty
2	218	0.58	0.80	27	empty
3	127	0.42	0.75	18	empty
4	101	0.36	0.74	21	empty
5	83	0.32	0.74	21	empty

Interfaces

1 interface between chains.

A–B · 585 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

5SBF · PanDDA analysis group deposition of ground-state model of SARS-CoV-2 NendoU · 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 5SBF · PDBe 5SBF · UniProt P0DTD1

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