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
- 1RVC
- Type
- protein + DNA
- Length
- 510 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(*AP*AP*AP*GP*AP*T)-3'); DNA (5'-D(*AP*TP*CP*TP*T)-3'); Protein (eco rv…
- UniProt
- P04390
- Ligands
- MG
- Pockets
- 8 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 33% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, E | DNA (5'-D(*AP*AP*AP*GP*AP*T)-3') | dna | 6 | — | — |
| D, F | DNA (5'-D(*AP*TP*CP*TP*T)-3') | dna | 5 | — | — |
| A, B | Protein (eco rv (E.C.3.1.21.4)) | protein | 244 | 33% helix, 30% strand | P04390 |
Ligands and binding sites
- MG · Magnesium ion · metal · 4 copies · chains D, A, B, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 87 | 0.75 | 0.97 | 22 | empty |
| 2 | 155 | 0.69 | 0.89 | 27 | MG |
| 3 | 119 | 0.59 | 0.85 | 27 | empty |
| 4 | 185 | 0.58 | 0.81 | 28 | empty |
| 5 | 160 | 0.57 | 0.82 | 28 | empty |
Interfaces
14 interfaces between chains.
- A–B · 2210 Ų buried · 31 hydrogen bonds · protein-protein
- F–B · 486 Ų buried · 8 hydrogen bonds · protein-nucleic
- D–A · 482 Ų buried · 9 hydrogen bonds · protein-nucleic
- C–B · 335 Ų buried · 10 hydrogen bonds · protein-nucleic
- E–A · 324 Ų buried · 9 hydrogen bonds · protein-nucleic
Compared structures
- 1RVC · 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 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 1RVC · PDBe 1RVC · UniProt P04390
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