Research workbench
X-ray structure of drosha in complex with the C-terminal tail of DGCR8.
Analyse X-ray structure of drosha in complex with the C-terminal tail of DGCR8. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5B16
- Type
- protein
- Length
- 770 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribonuclease 3,DROSHA,RIBONUCLEASE 3,DROSHA,RIBONUCLEASE 3; Microprocessor complex…
- EC
- 3.1.26.3
- UniProt
- Q9NRR4, Q8WYQ5
- Ligands
- ZN
- Pockets
- 13 · best druggability 0.64
Structure
x-ray diffraction · 3 distinct chains · 45% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribonuclease 3,DROSHA,RIBONUCLEASE 3,DROSHA,RIBONUCLEASE 3 (EC 3.1.26.3) | protein | 722 | 42% helix, 13% strand | Q9NRR4 |
| B | Microprocessor complex subunit DGCR8 | protein | 25 | 92% helix, 0% strand | Q8WYQ5 |
| C | Microprocessor complex subunit DGCR8 | protein | 23 | 74% helix, 0% strand | Q8WYQ5 |
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
13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 312 | 0.64 | 0.80 | 32 | empty |
| 2 | 139 | 0.58 | 0.84 | 27 | empty |
| 3 | 189 | 0.58 | 0.81 | 18 | empty |
| 4 | 131 | 0.58 | 0.84 | 23 | empty |
| 5 | 160 | 0.55 | 0.81 | 28 | empty |
Interfaces
2 interfaces between chains.
- A–B · 786 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 743 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 5B16 · X-ray structure of DROSHA in complex with the C-terminal tail of DGCR8. · 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 0.89
- 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 0.78
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 5B16 · PDBe 5B16 · UniProt Q9NRR4 · UniProt Q8WYQ5
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