MolNFT v1 · #11214 · protein
Crystal structure of MN(II)-complex of RNase III endonuclease domain from aquifex aeolicus at 2.10 ångström resolution
1JFZ · Ribonuclease III: “Crystal structure of MN(II)-complex of RNase III endonuclease domain from aquifex aeolicus at 2.10 ångström…”. X-ray diffraction, 1 ligand (MN), 4 pockets (best druggability 0.75). MolNFT v1 #11214 on GenesisL1…
- PDB
- 1JFZ
- Type
- protein
- Length
- 594 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribonuclease III
- EC
- 3.1.26.3
- UniProt
- O67082
- Ligands
- MN
- Pockets
- 4 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 67% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Ribonuclease III (EC 3.1.26.3) | protein | 148 | 66% helix, 1% strand | O67082 |
| B, C | Ribonuclease III (EC 3.1.26.3) | protein | 149 | 67% helix, 1% strand | O67082 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 4 copies · chains A, B, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 976 | 0.75 | 0.78 | 77 | MN |
| 2 | 198 | 0.44 | 0.73 | 27 | empty |
| 3 | 75 | 0.35 | 0.76 | 18 | empty |
| 4 | 70 | 0.33 | 0.76 | 15 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1236 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 1206 Ų buried · 22 hydrogen bonds · protein-protein
- A–D · 286 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 116 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 91 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 1JFZ · Crystal Structure of MN(II)-Complex of RNAse III Endonuclease Domain from Aquifex… · the same entry in another collection · chain A against A, TM-score 1.00
- O67082 · AlphaFold monomer V2.0 prediction for ribonuclease 3 (O67082) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 1JFZ · PDBe 1JFZ · UniProt O67082
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