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Crystal structure of E. COLI RNase E possessing M1 RNA fragments - catalytic domain
Analyse Crystal structure of E. COLI RNase E possessing M1 RNA fragments - catalytic… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2VRT
- Type
- protein + RNA
- Length
- 1,774 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribonuclease E; 5'-R(*UP*UP)-3'; 5'-R(*UP*UP*GP)-3'
- EC
- 3.1.4.-
- UniProt
- P21513
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 6 distinct chains · 34% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribonuclease E (EC 3.1.4.-) | protein | 468 | 33% helix, 25% strand | P21513 |
| B | Ribonuclease E (EC 3.1.4.-) | protein | 398 | 37% helix, 23% strand | P21513 |
| C | Ribonuclease E (EC 3.1.4.-) | protein | 411 | 35% helix, 24% strand | P21513 |
| D | Ribonuclease E (EC 3.1.4.-) | protein | 487 | 33% helix, 28% strand | P21513 |
| E, F | 5'-R(*UP*UP)-3' | rna | 2 | — | — |
| G, H | 5'-R(*UP*UP*GP)-3' | rna | 3 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 885 | 0.79 | 0.82 | 111 | empty |
| 2 | 641 | 0.76 | 0.82 | 82 | empty |
| 3 | 731 | 0.69 | 0.76 | 68 | empty |
| 4 | 339 | 0.69 | 0.82 | 46 | empty |
| 5 | 456 | 0.65 | 0.78 | 59 | empty |
Interfaces
9 interfaces between chains.
- C–D · 2748 Ų buried · 39 hydrogen bonds · protein-protein
- A–B · 2355 Ų buried · 20 hydrogen bonds · protein-protein
- B–D · 983 Ų buried · 26 hydrogen bonds · protein-protein
- A–C · 913 Ų buried · 21 hydrogen bonds · protein-protein
- C–H · 355 Ų buried · 9 hydrogen bonds · protein-nucleic
Compared structures
- 2VRT · Crystal Structure of E. coli RNase E possessing M1 RNA fragments - Catalytic Domain · the same entry in another collection · chain A against A, TM-score 1.00
- P21513 · AlphaFold monomer V2.0 prediction for ribonuclease E (P21513) · a predicted model of the same protein · chain C against A, TM-score 0.85
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 P21513
- Elsewhere: RCSB PDB 2VRT · PDBe 2VRT · UniProt P21513
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