MolNFT v1 · #126105 · protein

A CAF40-binding motif facilitates recruitment of the CCR4-not complex to mrnas targeted by drosophila roquin

5LSW · Cell differentiation protein RCD1 homolog: “A CAF40-binding motif facilitates recruitment of the CCR4-not complex to mrnas targeted by drosophila roquin”. X-ray diffraction, 1 ligand (SO4), 3 pockets (best druggability 0.87). MolNFT…

PDB: 5LSW
Type: protein
Length: 588 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cell differentiation protein RCD1 homolog; LD12033P
UniProt: Q92600, Q9VV48
Ligands: SO4
Pockets: 3 · best druggability 0.87

Structure

x-ray diffraction · 2 distinct chains · 75% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Cell differentiation protein RCD1 homolog	protein	273	75% helix, 0% strand	Q92600
B, D	LD12033P	protein	21	71% helix, 0% strand	Q9VV48

Ligands and binding sites

SO4 · Sulfate ion · ion · 4 copies · chains A, C
TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains A, C

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

Pockets

3 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	1102	0.87	0.88	94	empty
2	101	0.59	0.86	17	empty
3	61	0.39	0.80	15	empty

Interfaces

5 interfaces between chains.

A–B · 883 Å² buried · 8 hydrogen bonds · protein-protein
C–D · 831 Å² buried · 6 hydrogen bonds · protein-protein
A–C · 763 Å² buried · 17 hydrogen bonds · protein-protein
B–C · 190 Å² buried · 4 hydrogen bonds · protein-protein
A–D · 161 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

5LSW · A CAF40-binding motif facilitates recruitment of the CCR4-NOT complex to mRNAs targeted… · the same entry in another collection · chain A against A, TM-score 1.00
Q92600 · AlphaFold monomer V2.0 prediction for CCR4-not transcription complex subunit 9 (Q92600) · a predicted model of the same protein · chain A against A, TM-score 0.98

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 Q92600
Every structure of UniProt Q9VV48
Elsewhere: RCSB PDB 5LSW · PDBe 5LSW · UniProt Q92600 · UniProt Q9VV48

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