Research workbench
Pri-miRNA bound DROSHA-DGCR8 complex
Analyse Pri-miRNA bound DROSHA-DGCR8 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6LXD
- Type
- protein + RNA
- Length
- 1,035 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.9
- Source
- Homo sapiens; SYNTHETIC CONSTRUCT
- Molecule
- Ribonuclease 3; Microprocessor complex subunit DGCR8; RNA (102-mer)
- EC
- 3.1.26.3
- UniProt
- Q9NRR4, Q8WYQ5
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.89
Structure
electron microscopy · resolution 3.9 · 4 distinct chains · 45% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribonuclease 3 (EC 3.1.26.3) | protein | 918 | 42% helix, 9% strand | Q9NRR4 |
| B | Microprocessor complex subunit DGCR8 | protein | 24 | 92% helix, 0% strand | Q8WYQ5 |
| C | Microprocessor complex subunit DGCR8 | protein | 21 | 86% helix, 0% strand | Q8WYQ5 |
| D | RNA (102-mer) | rna | 72 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1002 | 0.89 | 0.91 | 112 | empty |
| 2 | 403 | 0.80 | 0.90 | 51 | empty |
| 3 | 473 | 0.78 | 0.87 | 47 | empty |
| 4 | 164 | 0.67 | 0.87 | 29 | empty |
| 5 | 115 | 0.59 | 0.86 | 20 | empty |
Interfaces
3 interfaces between chains.
- A–D · 3212 Ų buried · 51 hydrogen bonds · protein-nucleic
- A–C · 634 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 602 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6LXD · Pri-miRNA bound drosha-DGCR8 complex · the same entry in another collection · chain A against A, TM-score 1.00
- Q9NRR4 · AlphaFold monomer V2.0 prediction for ribonuclease 3 (Q9NRR4) · a predicted model of the same protein · chain A against A, TM-score 0.97
- Q8WYQ5 · AlphaFold monomer V2.0 prediction for microprocessor complex subunit DGCR8 (Q8WYQ5) · a predicted model of the same protein · chain B against A, TM-score 0.85
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 Q9NRR4
- Every structure of UniProt Q8WYQ5
- Elsewhere: RCSB PDB 6LXD · PDBe 6LXD · UniProt Q9NRR4 · UniProt Q8WYQ5
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