Research workbench
Human drosha and DGCR8 in complex with primary microrna (MP/RNA complex) - partially docked state
Analyse Human drosha and DGCR8 in complex with primary microrna (MP/RNA complex)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6V5C
- Type
- protein + RNA
- Length
- 1,402 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribonuclease 3; Microprocessor complex subunit DGCR8; Pri-mir-16-2 (66-mer)
- EC
- 3.1.26.3
- UniProt
- Q9NRR4, Q8WYQ5
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 4 distinct chains · 37% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribonuclease 3 (EC 3.1.26.3) | protein | 903 | 36% helix, 6% strand | Q9NRR4 |
| C | Microprocessor complex subunit DGCR8 | protein | 217 | 38% helix, 11% strand | Q8WYQ5 |
| B | Microprocessor complex subunit DGCR8 | protein | 216 | 38% helix, 9% strand | Q8WYQ5 |
| D | Pri-mir-16-2 (66-mer) | rna | 66 | — | — |
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1044 | 0.87 | 0.88 | 126 | empty |
| 2 | 368 | 0.84 | 0.93 | 73 | empty |
| 3 | 208 | 0.79 | 0.92 | 32 | empty |
| 4 | 105 | 0.78 | 0.97 | 27 | empty |
| 5 | 627 | 0.72 | 0.80 | 69 | empty |
Interfaces
6 interfaces between chains.
- A–D · 1246 Ų buried · 19 hydrogen bonds · protein-nucleic
- A–B · 1098 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 986 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 863 Ų buried · 18 hydrogen bonds · protein-nucleic
- B–D · 636 Ų buried · 11 hydrogen bonds · protein-nucleic
Compared structures
- 6V5C · Human Drosha and DGCR8 in complex with Primary MicroRNA (MP/RNA complex) - partially… · 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 0.82
- 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 0.72
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 6V5C · PDBe 6V5C · UniProt Q9NRR4 · UniProt Q8WYQ5
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