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Extended structure of the human DDX6 C-terminal domain in complex with an EDC3 fdf peptide

Analyse Extended structure of the human DDX6 C-terminal domain in complex with an EDC3… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6S8S
Type: protein
Length: 415 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Probable ATP-dependent RNA helicase DDX6; Enhancer of mRNA-decapping protein 3
EC: 3.6.4.13
UniProt: P26196, Q96F86
Ligands: PO4
Pockets: 8 · best druggability 0.52

Structure

x-ray diffraction · 3 distinct chains · 38% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Probable ATP-dependent RNA helicase DDX6 (EC 3.6.4.13)	protein	168	38% helix, 20% strand	P26196
B, D	Enhancer of mRNA-decapping protein 3	protein	37	43% helix, 0% strand	Q96F86
C	Probable ATP-dependent RNA helicase DDX6 (EC 3.6.4.13)	protein	173	38% helix, 21% strand	P26196

Ligands and binding sites

PO4 · Phosphate ion · ion · 9 copies · chains A, B, C, D
CXS · 3-cyclohexyl-1-propylsulfonic acid · additive · 5 copies · chains A, B, C, D

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	172	0.52	0.79	27	empty
2	146	0.47	0.77	27	empty
3	102	0.40	0.76	17	CXS, PO4
4	131	0.40	0.74	27	empty
5	74	0.37	0.77	15	CXS

Interfaces

5 interfaces between chains.

A–B · 1396 Å² buried · 13 hydrogen bonds · protein-protein
C–D · 1385 Å² buried · 13 hydrogen bonds · protein-protein
A–C · 773 Å² buried · 9 hydrogen bonds · protein-protein
B–C · 109 Å² buried · 1 hydrogen bond · protein-protein
A–D · 89 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

6S8S · Extended structure of the human DDX6 C-terminal domain in complex with an EDC3 FDF peptide · the same entry in another collection · chain D against D, TM-score 1.00
P26196 · AlphaFold monomer V2.0 prediction for probable ATP-dependent RNA helicase DDX6 (P26196) · a predicted model of the same protein · chain A against A, TM-score 0.94
Q96F86 · AlphaFold monomer V2.0 prediction for enhancer of mRNA-decapping protein 3 (Q96F86) · a predicted model of the same protein · chain B against A, TM-score 0.50

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 P26196
Every structure of UniProt Q96F86
Elsewhere: RCSB PDB 6S8S · PDBe 6S8S · UniProt P26196 · UniProt Q96F86

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