Research workbench
Ecorv bound to cognate DNA and MN2+
Analyse 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
- 1SX8
- Type
- protein + DNA
- Length
- 496 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*C*AP*AP*GP*AP*TP*AP*TP*CP*TP*T)-3'; Type II restriction enzyme ecorv
- EC
- 3.1.21.4
- UniProt
- P04390
- Ligands
- MN
- Pockets
- 2 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 33% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | 5'-D(*C*AP*AP*GP*AP*TP*AP*TP*CP*TP*T)-3' | dna | 10 | — | — |
| D | 5'-D(*C*AP*AP*GP*AP*TP*AP*TP*CP*TP*T)-3' | dna | 10 | — | — |
| A | Type II restriction enzyme ecorv (EC 3.1.21.4) | protein | 241 | 34% helix, 27% strand | P04390 |
| B | Type II restriction enzyme ecorv (EC 3.1.21.4) | protein | 235 | 33% helix, 31% strand | P04390 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 6 copies · chains C, A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 805 | 0.80 | 0.84 | 109 | MN |
| 2 | 242 | 0.58 | 0.79 | 28 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2013 Ų buried · 26 hydrogen bonds · protein-protein
- C–A · 744 Ų buried · 18 hydrogen bonds · protein-nucleic
- D–B · 695 Ų buried · 11 hydrogen bonds · protein-nucleic
- D–A · 497 Ų buried · 12 hydrogen bonds · protein-nucleic
- C–D · 417 Ų buried · 34 hydrogen bonds · nucleic-nucleic
Compared structures
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 1SX8 · PDBe 1SX8 · UniProt P04390
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