MolNFT v1 · #29125 · protein + RNA
Crystal structure of RNase III from aquifex aeolicus complexed with double stranded RNA at 2.8-ångström resolution
1YYW · 5'-R(*AP*AP*AP*UP*AP*UP*AP*UP*AP*UP*UP*U)-3': “Crystal structure of RNase III from aquifex aeolicus complexed with double stranded RNA at 2.8-ångström…”. X-ray diffraction, 11 pockets (best druggability 0.82). MolNFT v1 #29125 on…
- PDB
- 1YYW
- Type
- protein + RNA
- Length
- 971 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-R(*AP*AP*AP*UP*AP*UP*AP*UP*AP*UP*UP*U)-3'; Ribonuclease III
- EC
- 3.1.26.3
- UniProt
- O67082
- Pockets
- 11 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 53% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E, F, G, H, I, J, K, L | 5'-R(*AP*AP*AP*UP*AP*UP*AP*UP*AP*UP*UP*U)-3' | rna | 12 | — | — |
| A, B, D | Ribonuclease III (EC 3.1.26.3) | protein | 219 | 57% helix, 11% strand | O67082 |
| C | Ribonuclease III (EC 3.1.26.3) | protein | 218 | 50% helix, 11% strand | O67082 |
Pockets
11 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 839 | 0.82 | 0.85 | 81 | empty |
| 2 | 239 | 0.71 | 0.86 | 35 | empty |
| 3 | 988 | 0.67 | 0.74 | 47 | empty |
| 4 | 931 | 0.65 | 0.73 | 51 | empty |
| 5 | 156 | 0.61 | 0.84 | 25 | empty |
Interfaces
24 interfaces between chains.
- A–B · 1361 Ų buried · 26 hydrogen bonds · protein-protein
- C–D · 1310 Ų buried · 22 hydrogen bonds · protein-protein
- A–C · 596 Ų buried · 10 hydrogen bonds · protein-protein
- I–J · 527 Ų buried · 44 hydrogen bonds · nucleic-nucleic
- G–H · 520 Ų buried · 50 hydrogen bonds · nucleic-nucleic
Compared structures
- 1YYW · Crystal structure of RNase III from Aquifex aeolicus complexed with double stranded RNA… · the same entry in another collection · chain D against D, 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 O67082
- Elsewhere: RCSB PDB 1YYW · PDBe 1YYW · UniProt O67082
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