Research workbench

Csl (rbp-jk) bound to hes-1 nonconsensus site

Analyse Csl (rbp-jk) bound to hes-1 nonconsensus site in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3IAG
Type: protein + DNA
Length: 452 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 5'-D(*AP*AP*TP*CP*TP*TP*TP*CP*AP*CP*AP*CP*GP*AP*T)-3'…
UniProt: P31266
Ligands: XYL
Pockets: 9 · best druggability 0.74

Structure

x-ray diffraction · 3 distinct chains · 9% helix, 44% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	5'-D(APAPTPCPTPTPTPCPAPCPAPCPGPAP*T)-3'	dna	15	—	—
B	5'-D(TPTPAPTPCPGPTPGPTPGPAPAPAPGP*A)-3'	dna	15	—	—
C	Recombining binding protein suppressor of hairless	protein	422	9% helix, 44% strand	P31266

Ligands and binding sites

XYL · Xylitol · ligand · chains A, B
EDO · 1,2-ethanediol · additive · 6 copies · chains A, B, C

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

Pockets

9 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	577	0.74	0.81	45	EDO
2	222	0.53	0.77	29	empty
3	74	0.49	0.84	21	EDO
4	74	0.45	0.81	16	empty
5	95	0.43	0.78	23	empty

Interfaces

3 interfaces between chains.

A–B · 581 Å² buried · 58 hydrogen bonds · nucleic-nucleic
A–C · 563 Å² buried · 12 hydrogen bonds · protein-nucleic
B–C · 539 Å² buried · 13 hydrogen bonds · protein-nucleic

Compared structures

3IAG · CSL (RBP-Jk) bound to HES-1 nonconsensus site · the same entry in another collection · chain A against A, TM-score 1.00
P31266 · AlphaFold monomer V2.0 prediction for recombining binding protein suppressor of hairless… · a predicted model of the same protein · chain C 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 P31266
Elsewhere: RCSB PDB 3IAG · PDBe 3IAG · UniProt P31266

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.