Research workbench
Crystal structure of RNase III complexed with double-stranded RNA and AMP (type II cleavage)
Analyse Crystal structure of RNase III complexed with double-stranded RNA and AMP (type… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4M30
- Type
- protein + RNA
- Length
- 492 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribonuclease 3; RNA12
- EC
- 3.1.26.3
- UniProt
- O67082
- Ligands
- A, MG
- Pockets
- 7 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 60% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribonuclease 3 (EC 3.1.26.3) | protein | 220 | 60% helix, 11% strand | O67082 |
| B | Ribonuclease 3 (EC 3.1.26.3) | protein | 218 | 61% helix, 11% strand | O67082 |
| C, D | RNA12 | rna | 27 | — | — |
Ligands and binding sites
- A · Adenosine-5'-monophosphate · ligand · 2 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 9 copies · chains A, D, B, C
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 557 | 0.83 | 0.89 | 65 | MG, A |
| 2 | 151 | 0.63 | 0.86 | 24 | MG |
| 3 | 163 | 0.63 | 0.85 | 23 | MG |
| 4 | 53 | 0.37 | 0.81 | 12 | empty |
| 5 | 65 | 0.32 | 0.75 | 15 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1363 Ų buried · 24 hydrogen bonds · protein-protein
- A–D · 854 Ų buried · 21 hydrogen bonds · protein-nucleic
- B–C · 823 Ų buried · 22 hydrogen bonds · protein-nucleic
- B–D · 683 Ų buried · 13 hydrogen bonds · protein-nucleic
- A–C · 645 Ų buried · 14 hydrogen bonds · protein-nucleic
Compared structures
- 4M30 · Crystal structure of RNASE III complexed with double-stranded RNA AND AMP (TYPE II… · the same entry in another collection · chain B against B, TM-score 1.00
- O67082 · AlphaFold monomer V2.0 prediction for ribonuclease 3 (O67082) · a predicted model of the same protein · chain B against A, TM-score 0.95
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 4M30 · PDBe 4M30 · UniProt O67082
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