Research workbench
Ecorv bound to MN2+ and cognate DNA containing a 3'S substition at the cleavage site
Analyse Ecorv bound to MN2+ and cognate DNA containing a 3'S substition at the cleavage… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1EO4
- Type
- protein + DNA
- Length
- 494 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(*CP*AP*AP*GP*AP*(TSP)P*AP*TP*CP*TP*T)-3'); Type II restriction enzyme ecorv
- EC
- 3.1.21.4
- UniProt
- P04390
- Ligands
- MN
- Pockets
- 2 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 32% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | DNA (5'-D(*CP*AP*AP*GP*AP*(TSP)P*AP*TP*CP*TP*T)-3') | dna | 10 | — | — |
| D | DNA (5'-D(*CP*AP*AP*GP*AP*(TSP)P*AP*TP*CP*TP*T)-3') | dna | 10 | — | — |
| A | Type II restriction enzyme ecorv (EC 3.1.21.4) | protein | 238 | 29% helix, 28% strand | P04390 |
| B | Type II restriction enzyme ecorv (EC 3.1.21.4) | protein | 236 | 34% helix, 29% strand | P04390 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 5 copies · chains A, C, B
- ACY · Acetic acid · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 727 | 0.84 | 0.88 | 84 | MN |
| 2 | 551 | 0.68 | 0.78 | 71 | MN |
Interfaces
6 interfaces between chains.
- A–B · 1809 Ų buried · 22 hydrogen bonds · protein-protein
- C–A · 721 Ų buried · 16 hydrogen bonds · protein-nucleic
- D–B · 713 Ų buried · 13 hydrogen bonds · protein-nucleic
- C–B · 464 Ų buried · 12 hydrogen bonds · protein-nucleic
- D–A · 458 Ų buried · 8 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 1EO4 · Ecorv bound to MN2+ and cognate DNA containing a 3'S substition at the cleavage site · the same entry in another collection · chain D against D, 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 1.00
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 1EO4 · PDBe 1EO4 · UniProt P04390
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