Research workbench
Crystal structure of drosophila DHX36 helicase in complex with agggtttttt
Analyse Crystal structure of drosophila DHX36 helicase in complex with agggtttttt in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5N96
- Type
- protein + DNA
- Length
- 1,718 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CG9323, isoform a; DNA (5'-D(P*AP*GP*GP*GP*TP*TP*TP*TP*TP*T)-3')
- EC
- 3.6.1.3
- UniProt
- Q8SWT2
- Ligands
- MG
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 3 distinct chains · 47% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | CG9323, isoform a (EC 3.6.1.3) | protein | 849 | 47% helix, 15% strand | Q8SWT2 |
| B | CG9323, isoform a (EC 3.6.1.3) | protein | 851 | 47% helix, 17% strand | Q8SWT2 |
| C, D | DNA (5'-D(P*AP*GP*GP*GP*TP*TP*TP*TP*TP*T)-3') | dna | 9 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 860 | 0.88 | 0.90 | 88 | empty |
| 2 | 1168 | 0.87 | 0.88 | 85 | empty |
| 3 | 773 | 0.83 | 0.86 | 74 | empty |
| 4 | 1198 | 0.82 | 0.84 | 100 | empty |
| 5 | 172 | 0.73 | 0.90 | 30 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1564 Ų buried · 29 hydrogen bonds · protein-nucleic
- B–D · 1546 Ų buried · 29 hydrogen bonds · protein-nucleic
- A–B · 475 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 5N96 · Crystal Structure of Drosophila DHX36 helicase in complex with AGGGTTTTTT · the same entry in another collection · chain A against A, TM-score 1.00
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 Q8SWT2
- Elsewhere: RCSB PDB 5N96 · PDBe 5N96 · UniProt Q8SWT2
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