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Structure of the human DDX6 C-terminal domain in complex with an EDC3-fdf peptide
Analyse Structure of the human DDX6 C-terminal domain in complex with an EDC3-fdf… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2WAX
- Type
- protein
- Length
- 384 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP-dependent RNA helicase DDX6; Enhancer of mRNA-decapping protein 3
- EC
- 3.6.1.-
- UniProt
- P26196, Q96F86
- Ligands
- PO4
- Pockets
- 7 · best druggability 0.69
Structure
x-ray diffraction · 4 distinct chains · 42% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ATP-dependent RNA helicase DDX6 (EC 3.6.1.-) | protein | 161 | 40% helix, 22% strand | P26196 |
| B | Enhancer of mRNA-decapping protein 3 | protein | 30 | 53% helix, 0% strand | Q96F86 |
| C | ATP-dependent RNA helicase DDX6 (EC 3.6.1.-) | protein | 165 | 39% helix, 20% strand | P26196 |
| D | Enhancer of mRNA-decapping protein 3 | protein | 28 | 54% helix, 0% strand | Q96F86 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 4 copies · chains A, B, C
- CXS · 3-cyclohexyl-1-propylsulfonic acid · additive · 6 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 719 | 0.69 | 0.76 | 77 | CXS |
| 2 | 328 | 0.54 | 0.74 | 28 | empty |
| 3 | 94 | 0.43 | 0.78 | 15 | CXS |
| 4 | 76 | 0.39 | 0.78 | 16 | empty |
| 5 | 58 | 0.34 | 0.77 | 13 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1083 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 1004 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 432 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 34 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 13 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2WAX · Structure of the human DDX6 C-terminal domain in complex with an EDC3- FDF peptide · the same entry in another collection · chain C against C, 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 0.96
- Q96F86 · AlphaFold monomer V2.0 prediction for enhancer of mRNA-decapping protein 3 (Q96F86) · a predicted model of the same protein · chain D against A, TM-score 0.52
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 2WAX · PDBe 2WAX · UniProt P26196 · UniProt Q96F86
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