MolNFT v1 · #37837 · protein + DNA
Ecorv restriction endonuclease C-terminal deletion MUTANT/GATATC/CA2+
2GE5 · 5'-D(*AP*AP*AP*GP*AP*TP*AP*TP*CP*TP*T)-3': “Ecorv restriction endonuclease C-terminal deletion MUTANT/GATATC/CA2+”. X-ray diffraction, 1 ligand (CA), 5 pockets (best druggability 0.86). MolNFT v1 #37837 on GenesisL1: 3D structure…
- PDB
- 2GE5
- Type
- protein + DNA
- Length
- 460 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*AP*AP*AP*GP*AP*TP*AP*TP*CP*TP*T)-3'; Type II restriction enzyme ecorv
- EC
- 3.1.21.4
- UniProt
- P04390
- Ligands
- CA
- Pockets
- 5 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 27% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, D | 5'-D(*AP*AP*AP*GP*AP*TP*AP*TP*CP*TP*T)-3' | dna | 11 | — | — |
| A, B | Type II restriction enzyme ecorv (EC 3.1.21.4) | protein | 219 | 27% helix, 32% strand | P04390 |
Ligands and binding sites
- CA · Calcium ion · metal · chains C, A
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 | 657 | 0.86 | 0.91 | 77 | CA |
| 2 | 201 | 0.54 | 0.78 | 27 | empty |
| 3 | 198 | 0.53 | 0.78 | 30 | empty |
| 4 | 55 | 0.40 | 0.82 | 11 | empty |
| 5 | 54 | 0.33 | 0.78 | 10 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2030 Ų buried · 25 hydrogen bonds · protein-protein
- D–B · 722 Ų buried · 16 hydrogen bonds · protein-nucleic
- C–A · 711 Ų buried · 20 hydrogen bonds · protein-nucleic
- C–D · 454 Ų buried · 40 hydrogen bonds · nucleic-nucleic
- D–A · 407 Ų buried · 8 hydrogen bonds · protein-nucleic
Compared structures
- 2GE5 · EcoRV Restriction Endonuclease C-terminal deletion mutant/GATATC/Ca2+ · 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 2GE5 · PDBe 2GE5 · UniProt P04390
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