Research workbench
Crystal structure of wild type cre recombinase-loxp synapse
Analyse Crystal structure of wild type cre recombinase-loxp synapse in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1NZB
- Type
- protein + DNA
- Length
- 1,445 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Loxp DNA; Cre recombinase
- UniProt
- P06956
- Ligands
- MG, IOD
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 5 distinct chains · 54% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, G | Loxp DNA | dna | 37 | — | — |
| D, H | Loxp DNA | dna | 37 | — | — |
| A | Cre recombinase | protein | 332 | 54% helix, 5% strand | P06956 |
| B, F | Cre recombinase | protein | 322 | 54% helix, 7% strand | P06956 |
| E | Cre recombinase | protein | 321 | 54% helix, 3% strand | P06956 |
Ligands and binding sites
- MG · Magnesium ion · metal · 10 copies · chains C, D, A, G, H, F
- IOD · Iodide ion · ion · 2 copies · chains C, B, G, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1126 | 0.83 | 0.85 | 117 | MG |
| 2 | 588 | 0.77 | 0.84 | 65 | empty |
| 3 | 1091 | 0.74 | 0.77 | 114 | empty |
| 4 | 95 | 0.73 | 0.96 | 24 | empty |
| 5 | 851 | 0.72 | 0.77 | 73 | empty |
Interfaces
16 interfaces between chains.
- A–B · 2118 Ų buried · 17 hydrogen bonds · protein-protein
- E–F · 2097 Ų buried · 21 hydrogen bonds · protein-protein
- A–F · 1804 Ų buried · 22 hydrogen bonds · protein-protein
- B–E · 1689 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 1613 Ų buried · 150 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 1NZB · Crystal structure of wild type Cre recombinase-loxP synapse · 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 P06956
- Elsewhere: RCSB PDB 1NZB · PDBe 1NZB · UniProt P06956
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