MolNFT v1 · #156519 · protein + RNA
Crystal structure of caenorhabditis elegans dicer-related helicase 3 (drh-3) C-terminal domain with 5'-ppp 12-mer dsrna
6M6S · Dicer related helicase: “Crystal structure of caenorhabditis elegans dicer-related helicase 3 (drh-3) C-terminal domain with 5'-ppp…”. X-ray diffraction, 1 ligand (ZN), 4 pockets (best druggability 0.47). MolNFT v1 #156519 on…
- PDB
- 6M6S
- Type
- protein + RNA
- Length
- 346 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dicer related helicase; RNA (5'-R(*(GTP)P*GP*CP*GP*CP*GP*CP*GP*CP*GP*CP*C)-3')
- UniProt
- Q93413
- Ligands
- ZN
- Pockets
- 4 · best druggability 0.47
Structure
x-ray diffraction · 3 distinct chains · 32% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dicer related helicase | protein | 160 | 31% helix, 33% strand | Q93413 |
| B | Dicer related helicase | protein | 162 | 33% helix, 33% strand | Q93413 |
| C, D | RNA (5'-R(*(GTP)P*GP*CP*GP*CP*GP*CP*GP*CP*GP*CP*C)-3') | rna | 12 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 245 | 0.47 | 0.74 | 41 | empty |
| 2 | 241 | 0.44 | 0.72 | 21 | empty |
| 3 | 78 | 0.31 | 0.74 | 18 | empty |
| 4 | 56 | 0.28 | 0.75 | 14 | empty |
Interfaces
6 interfaces between chains.
- C–D · 614 Ų buried · 60 hydrogen bonds · nucleic-nucleic
- B–D · 520 Ų buried · 17 hydrogen bonds · protein-nucleic
- A–C · 457 Ų buried · 18 hydrogen bonds · protein-nucleic
- A–B · 368 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 190 Ų buried · 3 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 6M6S · Crystal structure of Caenorhabditis elegans Dicer-related helicase 3 (DRH-3) C-terminal… · 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 Q93413
- Elsewhere: RCSB PDB 6M6S · PDBe 6M6S · UniProt Q93413
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