MolNFT v1 · #46736 · protein + DNA
Restriction endonuclease bcni-cognate DNA substrate complex
2ODI · 5'-D(*AP*AP*CP*CP*CP*GP*GP*AP*GP*AP*C)-3': “Restriction endonuclease bcni-cognate DNA substrate complex”. X-ray diffraction, 2 ligands (CA, CL), 11 pockets (best druggability 0.62). MolNFT v1 #46736 on GenesisL1: 3D structure…
- PDB
- 2ODI
- Type
- protein + DNA
- Length
- 520 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*AP*AP*CP*CP*CP*GP*GP*AP*GP*AP*C)-3'; 5'-D(*CP*TP*CP*CP*GP*GP*GP*TP*TP*GP*T)-3'…
- UniProt
- Q8RNV8
- Ligands
- CA, CL
- Pockets
- 11 · best druggability 0.62
Structure
x-ray diffraction · 3 distinct chains · 19% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, E | 5'-D(*AP*AP*CP*CP*CP*GP*GP*AP*GP*AP*C)-3' | dna | 11 | — | — |
| D, F | 5'-D(*CP*TP*CP*CP*GP*GP*GP*TP*TP*GP*T)-3' | dna | 11 | — | — |
| A, B | R.BCNI | protein | 238 | 19% helix, 39% strand | Q8RNV8 |
Ligands and binding sites
- CA · Calcium ion · metal · 3 copies · chains C, A, E, B
- CL · Chloride ion · ion · 2 copies · chains C, A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 201 | 0.62 | 0.83 | 31 | empty |
| 2 | 290 | 0.57 | 0.77 | 35 | empty |
| 3 | 268 | 0.54 | 0.76 | 38 | CL |
| 4 | 225 | 0.52 | 0.77 | 25 | empty |
| 5 | 101 | 0.38 | 0.76 | 16 | empty |
Interfaces
10 interfaces between chains.
- E–B · 991 Ų buried · 27 hydrogen bonds · protein-nucleic
- C–A · 962 Ų buried · 24 hydrogen bonds · protein-nucleic
- D–A · 951 Ų buried · 23 hydrogen bonds · protein-nucleic
- F–B · 916 Ų buried · 22 hydrogen bonds · protein-nucleic
- E–F · 557 Ų buried · 42 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 12 modified (engineered).
Compared structures
- 2ODI · Restriction Endonuclease BCNI-Cognate DNA Substrate Complex · 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 Q8RNV8
- Elsewhere: RCSB PDB 2ODI · PDBe 2ODI · UniProt Q8RNV8
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