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
- 1OUQ
- Type
- protein + DNA
- Length
- 1,443 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Loxp DNA; Cre recombinase
- UniProt
- P06956
- Ligands
- A3P, MG, IOD
- Pockets
- 19 · best druggability 0.88
Structure
x-ray diffraction · 6 distinct chains · 55% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, G | Loxp DNA | dna | 15 | — | — |
| X, Y | Loxp DNA | dna | 21 | — | — |
| D, H | Loxp DNA | dna | 37 | — | — |
| A | Cre recombinase | protein | 332 | 54% helix, 4% strand | P06956 |
| B, F | Cre recombinase | protein | 322 | 55% helix, 5% strand | P06956 |
| E | Cre recombinase | protein | 321 | 56% helix, 3% strand | P06956 |
Ligands and binding sites
- A3P · Adenosine-3'-5'-diphosphate · ligand · 2 copies · chains C, X, D, B, G, Y, H, F
- MG · Magnesium ion · metal · 7 copies · chains D, H, F, X, A, G
- 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
19 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1153 | 0.88 | 0.90 | 116 | A3P, MG |
| 2 | 875 | 0.83 | 0.86 | 63 | A3P |
| 3 | 1036 | 0.78 | 0.80 | 99 | empty |
| 4 | 1113 | 0.75 | 0.78 | 98 | empty |
| 5 | 81 | 0.74 | 0.97 | 19 | empty |
Interfaces
20 interfaces between chains.
- E–F · 2110 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 2099 Ų buried · 18 hydrogen bonds · protein-protein
- A–F · 1778 Ų buried · 23 hydrogen bonds · protein-protein
- B–E · 1712 Ų buried · 21 hydrogen bonds · protein-protein
- D–B · 1469 Ų buried · 31 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 4 covalent, 2 modified (covalent ligand, nucleotide modification).
Compared structures
- 1OUQ · Crystal structure of wild-type Cre recombinase-loxP synapse · the same entry in another collection · chain X against X, 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 1OUQ · PDBe 1OUQ · UniProt P06956
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