Research workbench
Crystal structure of human GLE1 ctd-NUP42 gbm-DDX19B(AMPPNP) complex
Analyse Crystal structure of human GLE1 ctd-NUP42 gbm-DDX19B(AMPPNP) complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6B4J
- Type
- protein
- Length
- 1,564 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nucleoporin GLE1; Nucleoporin like 2; ATP-dependent RNA helicase DDX19B
- EC
- 3.6.4.13
- UniProt
- Q53GS7, Q9UMR2
- Ligands
- ANP, MG, PO4
- Pockets
- 17 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 48% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, A | Nucleoporin GLE1 | protein | 315 | 69% helix, 1% strand | Q53GS7 |
| C | Nucleoporin like 2 | protein | 44 | 23% helix, 0% strand | — |
| D | Nucleoporin like 2 | protein | 38 | 18% helix, 0% strand | — |
| E, F | ATP-dependent RNA helicase DDX19B (EC 3.6.4.13) | protein | 426 | 38% helix, 17% strand | Q9UMR2 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains E, F
- MG · Magnesium ion · metal · 2 copies · chains E, F
- PO4 · Phosphate ion · ion · 6 copies · chains B, A, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1198 | 0.82 | 0.84 | 141 | PO4, ANP |
| 2 | 600 | 0.79 | 0.85 | 82 | PO4, MG, ANP |
| 3 | 548 | 0.77 | 0.84 | 73 | empty |
| 4 | 330 | 0.77 | 0.88 | 51 | empty |
| 5 | 451 | 0.75 | 0.84 | 58 | empty |
Interfaces
10 interfaces between chains.
- B–F · 1487 Ų buried · 23 hydrogen bonds · protein-protein
- A–E · 1474 Ų buried · 14 hydrogen bonds · protein-protein
- E–F · 1259 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 1048 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 994 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 6B4J · Crystal structure of human Gle1 CTD-Nup42 GBM-DDX19B(AMPPNP) complex · the same entry in another collection · chain F against F, TM-score 1.00
- Q53GS7 · AlphaFold monomer V2.0 prediction for nucleoporin GLE1 (Q53GS7) · 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 E against A, TM-score 0.91
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 Q53GS7
- Every structure of UniProt Q9UMR2
- Elsewhere: RCSB PDB 6B4J · PDBe 6B4J · UniProt Q53GS7 · UniProt Q9UMR2
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