Research workbench

Csl (rbp-jk) bound to DNA

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

PDB: 3BRG
Type: protein + DNA
Length: 444 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA (5'- D(*DAP*DAP*DTP*DCP*DTP*DTP*DTP*DCP*DCP*DCP*DAP*DCP*DAP*DGP*DT)-3'); DNA (5'…
UniProt: P31266
Pockets: 10 · best druggability 0.73

Structure

x-ray diffraction · 3 distinct chains · 8% helix, 44% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA (5'- D(DAPDAPDTPDCPDTPDTPDTPDCPDCPDCPDAPDCPDAPDGP*DT)-3')	dna	15	—	—
B	DNA (5'- D(DTPDTPDAPDCPDTPDGPDTPDGPDGPDGPDAPDAPDAPDGP*DA)-3')	dna	15	—	—
C	Recombining binding protein suppressor of hairless	protein	414	8% helix, 44% strand	P31266

Ligands and binding sites

EDO · 1,2-ethanediol · additive · 12 copies · chains C, A, B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	421	0.73	0.83	59	EDO
2	269	0.55	0.77	25	empty
3	128	0.54	0.82	19	empty
4	148	0.44	0.76	26	EDO
5	89	0.40	0.77	20	EDO

Interfaces

3 interfaces between chains.

B–C · 626 Å² buried · 10 hydrogen bonds · protein-nucleic
A–B · 590 Å² buried · 55 hydrogen bonds · nucleic-nucleic
A–C · 511 Å² buried · 6 hydrogen bonds · protein-nucleic

Compared structures

3BRG · CSL (RBP-Jk) bound to DNA · 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 0.97

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 3BRG · PDBe 3BRG · UniProt P31266

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