Research workbench
Crystal structure of danio rerio SLIP1 in complex with DBP5
Analyse Crystal structure of danio rerio SLIP1 in complex with DBP5 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4JHJ
- Type
- protein
- Length
- 465 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MIF4G domain-containing protein B; DEAD/H (asp-glu-ala-ASP/HIS) box polypeptide 19 (DBP5…
- EC
- 3.6.1.-
- UniProt
- Q5EAQ1, Q7ZU28
- Pockets
- 4 · best druggability 0.65
Structure
x-ray diffraction · 3 distinct chains · 75% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MIF4G domain-containing protein B | protein | 216 | 77% helix, 2% strand | Q5EAQ1 |
| B | MIF4G domain-containing protein B | protein | 211 | 74% helix, 2% strand | Q5EAQ1 |
| C, D | DEAD/H (asp-glu-ala-ASP/HIS) box polypeptide 19 (DBP5 homolog, yeast) (EC 3.6.1.-) | protein | 19 | 68% helix, 0% strand | Q7ZU28 |
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 401 | 0.65 | 0.79 | 31 | empty |
| 2 | 53 | 0.33 | 0.78 | 13 | empty |
| 3 | 60 | 0.26 | 0.73 | 15 | empty |
| 4 | 54 | 0.25 | 0.73 | 15 | empty |
Interfaces
6 interfaces between chains.
- A–C · 692 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 638 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 431 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 421 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 68 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4JHJ · Crystal structure of Danio rerio Slip1 in complex with Dbp5 · the same entry in another collection · chain A against A, TM-score 1.00
- Q5EAQ1 · AlphaFold monomer V2.0 prediction for MIF4G domain-containing protein B (Q5EAQ1) · a predicted model of the same protein · chain B 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 Q5EAQ1
- Every structure of UniProt Q7ZU28
- Elsewhere: RCSB PDB 4JHJ · PDBe 4JHJ · UniProt Q5EAQ1 · UniProt Q7ZU28
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