Research workbench
Crystal structure of the nucleoporin NUP214 in complex with the dead- box helicase DDX19
Analyse Crystal structure of the nucleoporin NUP214 in complex with the dead- box… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3FMP
- Type
- protein
- Length
- 1,298 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nuclear pore complex protein NUP214; ATP-dependent RNA helicase DDX19B
- EC
- 3.6.1.-
- UniProt
- P35658, Q9UMR2
- Ligands
- ADP
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 15% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Nuclear pore complex protein NUP214 | protein | 420 | 4% helix, 40% strand | P35658 |
| B, D | ATP-dependent RNA helicase DDX19B (EC 3.6.1.-) | protein | 229 | 36% helix, 17% strand | Q9UMR2 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains B, 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, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 826 | 0.79 | 0.82 | 49 | empty |
| 2 | 844 | 0.79 | 0.82 | 52 | empty |
| 3 | 484 | 0.75 | 0.84 | 61 | empty |
| 4 | 393 | 0.71 | 0.83 | 50 | empty |
| 5 | 57 | 0.68 | 0.96 | 21 | empty |
Interfaces
3 interfaces between chains.
- C–D · 1090 Ų buried · 33 hydrogen bonds · protein-protein
- A–B · 1087 Ų buried · 33 hydrogen bonds · protein-protein
- B–C · 552 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 3FMP · Crystal structure of the nucleoporin Nup214 in complex with the DEAD-box helicase Ddx19 · the same entry in another collection · chain A against A, TM-score 1.00
- P35658 · AlphaFold monomer V2.0 prediction for nuclear pore complex protein NUP214 (P35658) · a predicted model of the same protein · chain A against A, TM-score 0.99
- Q9UMR2 · AlphaFold monomer V2.0 prediction for ATP-dependent RNA helicase DDX19B (Q9UMR2) · a predicted model of the same protein · chain D 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 P35658
- Every structure of UniProt Q9UMR2
- Elsewhere: RCSB PDB 3FMP · PDBe 3FMP · UniProt P35658 · UniProt Q9UMR2
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