MolNFT v1 · #166927 · protein + RNA
Human drosha and DGCR8 in complex with primary microrna (MP/RNA complex) - active state
6V5B · Ribonuclease 3: “Human drosha and DGCR8 in complex with primary microrna (MP/RNA complex) - active state”. Electron microscopy, 2 ligands (ZN, CA), 20 pockets (best druggability 0.89). MolNFT v1 #166927 on GenesisL1: 3D structure…
- PDB
- 6V5B
- Type
- protein + RNA
- Length
- 1,419 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 (78-mer)
- EC
- 3.1.26.3
- UniProt
- Q9NRR4, Q8WYQ5
- Ligands
- ZN, CA
- Pockets
- 20 · best druggability 0.89
Structure
electron microscopy · 4 distinct chains · 39% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribonuclease 3 (EC 3.1.26.3) | protein | 908 | 39% helix, 8% strand | Q9NRR4 |
| C | Microprocessor complex subunit DGCR8 | protein | 217 | 40% helix, 12% strand | Q8WYQ5 |
| B | Microprocessor complex subunit DGCR8 | protein | 216 | 36% helix, 16% strand | Q8WYQ5 |
| D | Pri-mir-16-2 (78-mer) | rna | 78 | — | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1099 | 0.89 | 0.91 | 131 | empty |
| 2 | 362 | 0.79 | 0.89 | 52 | empty |
| 3 | 626 | 0.74 | 0.81 | 54 | empty |
| 4 | 580 | 0.73 | 0.81 | 69 | empty |
| 5 | 578 | 0.70 | 0.80 | 39 | empty |
Interfaces
6 interfaces between chains.
- A–D · 3494 Ų buried · 55 hydrogen bonds · protein-nucleic
- A–B · 1015 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 952 Ų buried · 2 hydrogen bonds · protein-protein
- C–D · 708 Ų buried · 14 hydrogen bonds · protein-nucleic
- B–D · 622 Ų buried · 8 hydrogen bonds · protein-nucleic
Compared structures
- 6V5B · Human Drosha and DGCR8 in complex with Primary MicroRNA (MP/RNA complex) - Active state · 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 0.98
- 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 0.71
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 6V5B · PDBe 6V5B · UniProt Q9NRR4 · UniProt Q8WYQ5
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