Research workbench

Drosophila Bag-of-marbles CBM peptide bound to human CAF40

Analyse Drosophila Bag-of-marbles CBM peptide bound to human CAF40 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5ONB
Type: protein
Length: 1,165 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 3
Source: Homo sapiens; SYNTHETIC CONSTRUCT
Molecule: CCR4-NOT transcription complex subunit 9; Protein bag-of-marbles
UniProt: Q92600, P22745
Pockets: 20 · best druggability 0.81

Structure

x-ray diffraction · resolution 3 · 6 distinct chains · 79% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, G	CCR4-NOT transcription complex subunit 9	protein	270	78% helix, 0% strand	Q92600
B, D	Protein bag-of-marbles	protein	22	86% helix, 0% strand	P22745
C	CCR4-NOT transcription complex subunit 9	protein	268	79% helix, 0% strand	Q92600
E	CCR4-NOT transcription complex subunit 9	protein	269	79% helix, 0% strand	Q92600
F	Protein bag-of-marbles	protein	23	78% helix, 0% strand	P22745
H	Protein bag-of-marbles	protein	21	90% helix, 0% strand	P22745

Ligands and binding sites

GOL · Glycerol · additive · chains G, H

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

Pockets

20 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	847	0.81	0.84	94	empty
2	384	0.65	0.79	48	empty
3	152	0.55	0.81	27	empty
4	166	0.49	0.77	18	empty
5	165	0.47	0.76	19	empty

Interfaces

10 interfaces between chains.

A–C · 1118 Å² buried · 3 hydrogen bonds · protein-protein
E–F · 1003 Å² buried · 7 hydrogen bonds · protein-protein
A–B · 998 Å² buried · 9 hydrogen bonds · protein-protein
E–G · 992 Å² buried · 1 hydrogen bond · protein-protein
G–H · 946 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

5ONB · Drosophila bag-of-marbles cbm peptide bound to human CAF40 · the same entry in another collection · chain H against H, 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 0.99

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 P22745
Elsewhere: RCSB PDB 5ONB · PDBe 5ONB · UniProt Q92600 · UniProt P22745

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