Research workbench

The cryo-EM structure of the DDX42-SF3b complex

Analyse The cryo-EM structure of the DDX42-SF3b complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7EVN
Type: protein
Length: 2,649 residues
Chains: 5
Method: electron microscopy
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 2.6
Source: Homo sapiens
Molecule: Splicing factor 3B subunit 5; Splicing factor 3B subunit 1; PHD finger-like…
EC: 3.6.4.13
UniProt: Q9BWJ5, O75533, Q7RTV0, Q15393, Q86XP3
Ligands: ZN
Pockets: 20 · best druggability 0.86

Structure

electron microscopy · resolution 2.6 · 5 distinct chains · 38% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	Splicing factor 3B subunit 5	protein	78	60% helix, 0% strand	Q9BWJ5
C	Splicing factor 3B subunit 1	protein	815	77% helix, 0% strand	O75533
D	PHD finger-like domain-containing protein 5A	protein	93	12% helix, 27% strand	Q7RTV0
A	Splicing factor 3B subunit 3	protein	1177	7% helix, 46% strand	Q15393
E	ATP-dependent RNA helicase DDX42 (EC 3.6.4.13)	protein	486	48% helix, 14% strand	Q86XP3

Ligands and binding sites

ZN · Zinc ion · metal · 3 copies · chains D

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

Pockets

20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1074	0.86	0.87	78	empty
2	978	0.84	0.85	108	empty
3	948	0.82	0.84	133	empty
4	576	0.81	0.87	64	empty
5	379	0.81	0.90	70	empty

Interfaces

10 interfaces between chains.

C–E · 2311 Å² buried · 26 hydrogen bonds · protein-protein
B–A · 2275 Å² buried · 25 hydrogen bonds · protein-protein
C–A · 2108 Å² buried · 19 hydrogen bonds · protein-protein
B–C · 1609 Å² buried · 17 hydrogen bonds · protein-protein
C–D · 1177 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

7EVN · The cryo-EM structure of the DDX42-SF3B complex · the same entry in another collection · chain E against E, TM-score 1.00
Q15393 · AlphaFold monomer V2.0 prediction for splicing factor 3B subunit 3 (Q15393) · a predicted model of the same protein · chain A against A, TM-score 0.96
Q7RTV0 · AlphaFold monomer V2.0 prediction for phd finger-like domain- containing protein 5A… · a predicted model of the same protein · chain D against A, TM-score 0.89
Q9BWJ5 · AlphaFold monomer V2.0 prediction for splicing factor 3B subunit 5 (Q9BWJ5) · a predicted model of the same protein · chain B against A, TM-score 0.85
O75533 · AlphaFold monomer V2.0 prediction for splicing factor 3B subunit 1 (O75533) · a predicted model of the same protein · chain C against A, TM-score 0.79
Q86XP3 · AlphaFold monomer V2.0 prediction for ATP-dependent RNA helicase DDX42 (Q86XP3) · a predicted model of the same protein · chain E against A, TM-score 0.54

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 Q9BWJ5
Every structure of UniProt O75533
Every structure of UniProt Q7RTV0
Every structure of UniProt Q15393
Every structure of UniProt Q86XP3
Elsewhere: RCSB PDB 7EVN · PDBe 7EVN · UniProt Q9BWJ5 · UniProt O75533 · UniProt Q7RTV0 · UniProt Q15393 · UniProt Q86XP3

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