Research workbench
The crystal structure of ecorv endonuclease and of its complexes with cognate and non-cognate DNA segments
Analyse The crystal structure of ecorv endonuclease and of its complexes with cognate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4RVE
- Type
- protein + DNA
- Length
- 750 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(*GP*GP*GP*AP*TP*AP*TP*CP*CP*C)-3'); Protein (eco rv (E.C.3.1.21.4))
- UniProt
- P04390
- Pockets
- 7 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D, E, F | DNA (5'-D(*GP*GP*GP*AP*TP*AP*TP*CP*CP*C)-3') | dna | 10 | — | — |
| A, B, C | Protein (eco rv (E.C.3.1.21.4)) | protein | 240 | 30% helix, 29% strand | P04390 |
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 | 222 | 0.81 | 0.95 | 32 | empty |
| 2 | 492 | 0.78 | 0.86 | 61 | empty |
| 3 | 653 | 0.70 | 0.79 | 86 | empty |
| 4 | 141 | 0.45 | 0.77 | 26 | empty |
| 5 | 117 | 0.41 | 0.76 | 16 | empty |
Interfaces
8 interfaces between chains.
- A–B · 1710 Ų buried · 18 hydrogen bonds · protein-protein
- F–C · 832 Ų buried · 17 hydrogen bonds · protein-nucleic
- E–A · 828 Ų buried · 20 hydrogen bonds · protein-nucleic
- D–B · 778 Ų buried · 11 hydrogen bonds · protein-nucleic
- D–A · 472 Ų buried · 10 hydrogen bonds · protein-nucleic
Compared structures
- 4RVE · The crystal structure of ecorv endonuclease and of its complexes with cognate and… · the same entry in another collection · chain F against F, TM-score 1.00
- P04390 · AlphaFold monomer V2.0 prediction for type-2 restriction enzyme ecorv (P04390) · a predicted model of the same protein · chain A 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 P04390
- Elsewhere: RCSB PDB 4RVE · PDBe 4RVE · UniProt P04390
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