Research workbench
MG2+ binding to the active site of eco rv endonuclease: a crystallographic study of complexes with substrate and product DNA at 2 ångströms resolution
Analyse MG2+ binding to the active site of eco rv endonuclease: a crystallographic… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1RVA
- 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'); Protein (eco rv (E.C.3.1.21.4))
- UniProt
- P04390
- Pockets
- 7 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 29% 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 | Protein (eco rv (E.C.3.1.21.4)) | protein | 244 | 34% helix, 29% strand | P04390 |
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 533 | 0.85 | 0.91 | 70 | empty |
| 2 | 164 | 0.58 | 0.82 | 26 | empty |
| 3 | 174 | 0.57 | 0.81 | 27 | empty |
| 4 | 256 | 0.56 | 0.78 | 36 | empty |
| 5 | 57 | 0.34 | 0.79 | 12 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2219 Ų buried · 26 hydrogen bonds · protein-protein
- C–A · 761 Ų buried · 13 hydrogen bonds · protein-nucleic
- D–B · 754 Ų buried · 12 hydrogen bonds · protein-nucleic
- C–B · 564 Ų buried · 14 hydrogen bonds · protein-nucleic
- D–A · 535 Ų buried · 9 hydrogen bonds · protein-nucleic
Compared structures
- 1RVA · MG2+ binding to the active site of eco rv endonuclease: a crystallographic study of… · 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 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 1RVA · PDBe 1RVA · UniProt P04390
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