MolNFT v1 · #55077 · protein + RNA

Structure of CRISPR endoribonuclease CSE3 bound to 20 nt RNA

2Y8W: “Structure of CRISPR endoribonuclease CSE3 bound to 20 nt RNA”. X-ray diffraction, 3 pockets (best druggability 0.41). MolNFT v1 #55077 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2Y8W
Type: protein + RNA
Length: 235 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: CSE3; 5'-R(*UP*CP*CP*CP*CP*AP*CP*GP*CP*GP*UP*GP*UP*GP *GP*GP*DGP*AP*UP*G)-3'
UniProt: Q53WG9
Pockets: 3 · best druggability 0.41

Structure

x-ray diffraction · 2 distinct chains · 26% helix, 36% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	CSE3	protein	215	26% helix, 36% strand	Q53WG9
B	5'-R(UPCPCPCPCPAPCPGPCPGPUPGPUPGP GPGPDGPAPUPG)-3'	rna	20	—	—

Pockets

3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	60	0.41	0.81	17	empty
2	101	0.37	0.75	24	empty
3	50	0.32	0.78	14	empty

Interfaces

1 interface between chains.

A–B · 1654 Å² buried · 68 hydrogen bonds · protein-nucleic

Compared structures

2Y8W · Structure of CRISPR endoribonuclease Cse3 bound to 20 nt RNA · the same entry in another collection · chain A against A, TM-score 1.00
Q53WG9 · AlphaFold monomer V2.0 prediction for CRISPR-associated endoribonuclease CSE3 (Q53WG9) · a predicted model of the same protein · chain A against A, TM-score 0.95

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 Q53WG9
Elsewhere: RCSB PDB 2Y8W · PDBe 2Y8W · UniProt Q53WG9

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