MolNFT v1 · #20956 · protein + DNA
MG2+ binding to the active site of eco rv endonuclease: a crystallographic study of complexes with substrate and product DNA at 2 ångströms resolution
1RVB · DNA (5'-D(*AP*AP*AP*GP*AP*TP*AP*TP*CP*TP*T)-3'): “MG2+ binding to the active site of eco rv endonuclease: a crystallographic study of complexes with substrate…”. X-ray diffraction, 1 ligand (MG), 6 pockets (best druggability 0.83).…
- PDB
- 1RVB
- 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
- Ligands
- MG
- Pockets
- 6 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 34% 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 | Protein (eco rv (E.C.3.1.21.4)) | protein | 244 | 34% helix, 27% strand | P04390 |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains D, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 474 | 0.83 | 0.90 | 77 | MG |
| 2 | 175 | 0.58 | 0.82 | 28 | empty |
| 3 | 177 | 0.58 | 0.82 | 26 | empty |
| 4 | 251 | 0.54 | 0.77 | 30 | empty |
| 5 | 54 | 0.30 | 0.77 | 10 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2256 Ų buried · 24 hydrogen bonds · protein-protein
- C–A · 776 Ų buried · 13 hydrogen bonds · protein-nucleic
- D–B · 758 Ų buried · 15 hydrogen bonds · protein-nucleic
- C–B · 555 Ų buried · 13 hydrogen bonds · protein-nucleic
- D–A · 523 Ų buried · 10 hydrogen bonds · protein-nucleic
Compared structures
- 1RVB · 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 1RVB · PDBe 1RVB · UniProt P04390
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.