MolNFT v1 · #50840 · protein + DNA
The crystal structure of ecorv endonuclease and of its complexes with cognate and non-cognate DNA segments
2RVE · DNA (5'-D(*CP*GP*AP*GP*CP*TP*CP*G)-3'): “The crystal structure of ecorv endonuclease and of its complexes with cognate and non-cognate DNA segments”. X-ray diffraction, 3 pockets (best druggability 0.86). MolNFT v1 #50840 on…
- PDB
- 2RVE
- Type
- protein + DNA
- Length
- 457 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(*CP*GP*AP*GP*CP*TP*CP*G)-3'); Protein (eco rv (E.C.3.1.21.4))
- UniProt
- P04390
- Pockets
- 3 · best druggability 0.86
Structure
x-ray diffraction · 3 distinct chains · 31% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, D, E, F | DNA (5'-D(*CP*GP*AP*GP*CP*TP*CP*G)-3') | dna | 8 | — | — |
| A | Protein (eco rv (E.C.3.1.21.4)) | protein | 213 | 30% helix, 32% strand | P04390 |
| B | Protein (eco rv (E.C.3.1.21.4)) | protein | 212 | 32% helix, 26% strand | P04390 |
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1195 | 0.86 | 0.87 | 114 | empty |
| 2 | 69 | 0.39 | 0.80 | 17 | empty |
| 3 | 79 | 0.38 | 0.78 | 14 | empty |
Interfaces
14 interfaces between chains.
- A–B · 1141 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 393 Ų buried · 47 hydrogen bonds · nucleic-nucleic
- E–F · 381 Ų buried · 45 hydrogen bonds · nucleic-nucleic
- D–B · 279 Ų buried · 2 hydrogen bonds · protein-nucleic
- F–A · 242 Ų buried · 4 hydrogen bonds · protein-nucleic
Compared structures
- 2RVE · The crystal structure of ecorv endonuclease and of its complexes with cognate and… · the same entry in another collection · chain B against B, 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 B against A, TM-score 0.97
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 2RVE · PDBe 2RVE · UniProt P04390
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