MolNFT v1 · #5638 · protein + DNA
Inhibition of ecorv endonuclease by deoxyribo-3'-S-phosphorothiolates: a high resolution X-ray crystallographic study
1EO3 · DNA (5'-D(*CP*AP*AP*GP*AP*(TSP)P*AP*TP*CP*TP*T)-3'): “Inhibition of ecorv endonuclease by deoxyribo-3'-S-phosphorothiolates: a high resolution X-ray…”. X-ray diffraction, 1 ligand (MG), 5 pockets (best druggability 0.84). MolNFT v1…
- PDB
- 1EO3
- Type
- protein + DNA
- Length
- 497 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
- MG
- Pockets
- 5 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 31% helix, 27% 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 | 241 | 30% helix, 27% strand | P04390 |
| B | Type II restriction enzyme ecorv (EC 3.1.21.4) | protein | 236 | 32% helix, 27% strand | P04390 |
Ligands and binding sites
- MG · Magnesium ion · metal · 4 copies · chains A, C, B, D
- 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
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 764 | 0.84 | 0.87 | 83 | MG |
| 2 | 166 | 0.56 | 0.81 | 26 | empty |
| 3 | 226 | 0.54 | 0.78 | 36 | empty |
| 4 | 166 | 0.46 | 0.76 | 25 | empty |
| 5 | 52 | 0.28 | 0.76 | 10 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1803 Ų buried · 21 hydrogen bonds · protein-protein
- C–A · 733 Ų buried · 15 hydrogen bonds · protein-nucleic
- D–B · 670 Ų buried · 10 hydrogen bonds · protein-nucleic
- D–A · 456 Ų buried · 10 hydrogen bonds · protein-nucleic
- C–B · 437 Ų buried · 14 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 1EO3 · Inhibition of ecorv endonuclease by deoxyribo-3'-S-phosphorothiolates: a high resolution… · the same entry in another collection · chain C against C, 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 0.99
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 1EO3 · PDBe 1EO3 · UniProt P04390
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