Research workbench
Structure of the K38A mutant of ecorv bound to cognate DNA and MN2+
Analyse Structure of the K38A mutant of ecorv bound to cognate DNA and MN2+ in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1STX
- Type
- protein + DNA
- Length
- 510 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*AP*AP*AP*GP*AP*T)-3'; 5'-D(P*AP*TP*CP*TP*T)-3'; Type II restriction enzyme ecorv
- EC
- 3.1.21.4
- UniProt
- P04390
- Ligands
- MN
- Pockets
- 4 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 32% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, E | 5'-D(*AP*AP*AP*GP*AP*T)-3' | dna | 6 | — | — |
| D, F | 5'-D(P*AP*TP*CP*TP*T)-3' | dna | 5 | — | — |
| A, B | Type II restriction enzyme ecorv (EC 3.1.21.4) | protein | 244 | 32% helix, 27% strand | P04390 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 6 copies · chains D, A, F, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 475 | 0.84 | 0.91 | 67 | MN |
| 2 | 210 | 0.56 | 0.79 | 26 | MN |
| 3 | 212 | 0.54 | 0.78 | 27 | empty |
| 4 | 185 | 0.52 | 0.78 | 34 | empty |
Interfaces
14 interfaces between chains.
- A–B · 2000 Ų buried · 21 hydrogen bonds · protein-protein
- D–A · 443 Ų buried · 8 hydrogen bonds · protein-nucleic
- F–B · 437 Ų buried · 14 hydrogen bonds · protein-nucleic
- E–B · 341 Ų buried · 6 hydrogen bonds · protein-nucleic
- C–A · 340 Ų buried · 4 hydrogen bonds · protein-nucleic
Compared structures
- 1STX · Structure of the K38A mutant of EcoRV bound to cognate DNA and Mn2+ · the same entry in another collection · chain E against E, 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 1STX · PDBe 1STX · UniProt P04390
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