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
- 1B97
- 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
- 4 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 27% 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 | 33% helix, 27% strand | P04390 |
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 461 | 0.85 | 0.93 | 66 | empty |
| 2 | 431 | 0.66 | 0.79 | 57 | empty |
| 3 | 154 | 0.56 | 0.82 | 29 | empty |
| 4 | 60 | 0.29 | 0.75 | 13 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2181 Ų buried · 24 hydrogen bonds · protein-protein
- C–A · 747 Ų buried · 12 hydrogen bonds · protein-nucleic
- D–B · 737 Ų buried · 12 hydrogen bonds · protein-nucleic
- C–B · 524 Ų buried · 12 hydrogen bonds · protein-nucleic
- D–A · 505 Ų buried · 9 hydrogen bonds · protein-nucleic
Compared structures
- 1B97 · 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 1B97 · PDBe 1B97 · UniProt P04390
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