Research workbench
Analysis of a mutational hot-spot in the ecorv restriction endonuclease: a catalytic role for a main chain carbonyl group
Analyse Analysis of a mutational hot-spot in the ecorv restriction endonuclease: a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1B96
- Type
- protein + DNA
- Length
- 510 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(*AP*AP*AP*GP*AP*TP*AP*TP*CP*TP*T)-3'); Restriction endonuclease ecorv
- EC
- 3.1.21.4
- UniProt
- P04390
- Pockets
- 6 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, D | DNA (5'-D(*AP*AP*AP*GP*AP*TP*AP*TP*CP*TP*T)-3') | dna | 11 | — | — |
| A, B | Restriction endonuclease ecorv (EC 3.1.21.4) | protein | 244 | 35% helix, 30% strand | P04390 |
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 464 | 0.85 | 0.92 | 70 | empty |
| 2 | 294 | 0.60 | 0.79 | 50 | empty |
| 3 | 116 | 0.56 | 0.84 | 25 | empty |
| 4 | 68 | 0.45 | 0.82 | 18 | empty |
| 5 | 52 | 0.29 | 0.76 | 10 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2127 Ų buried · 32 hydrogen bonds · protein-protein
- C–A · 762 Ų buried · 14 hydrogen bonds · protein-nucleic
- D–B · 747 Ų buried · 14 hydrogen bonds · protein-nucleic
- D–A · 531 Ų buried · 14 hydrogen bonds · protein-nucleic
- C–B · 523 Ų buried · 12 hydrogen bonds · protein-nucleic
Compared structures
- 1B96 · Analysis of a mutational hot-spot in the ecorv restriction endonuclease: a catalytic role… · 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 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 1B96 · PDBe 1B96 · UniProt P04390
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