MolNFT v1 · #127852 · protein + DNA
Crystal structure of drosophila DHX36 helicase in complex with ctctccctt
5N8Z · CG9323, isoform a: “Crystal structure of drosophila DHX36 helicase in complex with ctctccctt”. X-ray diffraction, 1 ligand (PO4), 20 pockets (best druggability 0.86). MolNFT v1 #127852 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5N8Z
- Type
- protein + DNA
- Length
- 1,716 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CG9323, isoform a; DNA (5'-D(P*CP*TP*CP*TP*CP*CP*CP*TP*T)-3')
- EC
- 3.6.1.3
- UniProt
- Q8SWT2
- Ligands
- PO4
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | CG9323, isoform a (EC 3.6.1.3) | protein | 849 | 47% helix, 16% strand | Q8SWT2 |
| C, D | DNA (5'-D(P*CP*TP*CP*TP*CP*CP*CP*TP*T)-3') | dna | 9 | — | — |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 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, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 666 | 0.86 | 0.90 | 72 | empty |
| 2 | 545 | 0.85 | 0.91 | 66 | empty |
| 3 | 538 | 0.84 | 0.90 | 52 | empty |
| 4 | 434 | 0.82 | 0.90 | 38 | empty |
| 5 | 190 | 0.72 | 0.88 | 31 | empty |
Interfaces
3 interfaces between chains.
- B–D · 1517 Ų buried · 25 hydrogen bonds · protein-nucleic
- A–C · 1509 Ų buried · 19 hydrogen bonds · protein-nucleic
- A–B · 510 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 5N8Z · Crystal Structure of Drosophila DHX36 helicase in complex with CTCTCCCTT · 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 5N8Z · PDBe 5N8Z · UniProt Q8SWT2
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