Research workbench
Crystal structure of noti restriction endonuclease bound to cognate DNA
Analyse Crystal structure of noti restriction endonuclease bound to cognate DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3C25
- Type
- protein + DNA
- Length
- 751 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'- D(*DCP*DGP*DGP*DAP*DGP*DGP*DCP*DGP*DCP*DGP*DGP*DCP*DCP*DGP*DCP*DGP*DC…
- UniProt
- Q2I6W2
- Ligands
- CA, FE
- Pockets
- 8 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 34% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | DNA (5'- D(*DCP*DGP*DGP*DAP*DGP*DGP*DCP*DGP*DCP*DGP*DGP*DCP*DCP*DGP*DCP*DGP*DC P*DCP*DGP*DCP*DCP*DG)-3') | dna | 22 | — | — |
| D | DNA (5'- D(*DCP*DGP*DGP*DCP*DGP*DGP*DCP*DGP*DCP*DGP*DGP*DCP*DCP*DGP*DCP*DGP*DC P*DCP*DTP*DCP*DCP*DG)-3') | dna | 22 | — | — |
| A | Noti restriction endonuclease | protein | 354 | 34% helix, 27% strand | Q2I6W2 |
| B | Noti restriction endonuclease | protein | 353 | 34% helix, 27% strand | Q2I6W2 |
Ligands and binding sites
- CA · Calcium ion · metal · 4 copies · chains D, A, C, B
- FE · Fe (III) ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 710 | 0.83 | 0.87 | 62 | CA |
| 2 | 261 | 0.58 | 0.79 | 26 | empty |
| 3 | 256 | 0.56 | 0.78 | 27 | empty |
| 4 | 66 | 0.41 | 0.80 | 14 | empty |
| 5 | 95 | 0.38 | 0.76 | 23 | empty |
Interfaces
6 interfaces between chains.
- A–B · 3621 Ų buried · 36 hydrogen bonds · protein-protein
- C–D · 1051 Ų buried · 107 hydrogen bonds · nucleic-nucleic
- D–A · 961 Ų buried · 27 hydrogen bonds · protein-nucleic
- C–B · 958 Ų buried · 25 hydrogen bonds · protein-nucleic
- C–A · 683 Ų buried · 11 hydrogen bonds · protein-nucleic
Compared structures
- 3C25 · Crystal Structure of NotI Restriction Endonuclease Bound to Cognate DNA · the same entry in another collection · chain C against C, 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 Q2I6W2
- Elsewhere: RCSB PDB 3C25 · PDBe 3C25 · UniProt Q2I6W2
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