Research workbench
Asymmetric DNA-bending in the cre-loxp site-specific recombination synapse
Analyse Asymmetric DNA-bending in the cre-loxp site-specific recombination synapse in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5CRX
- Type
- protein + DNA
- Length
- 659 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (35-mer); Protein (bacteriophage P1 cre gene)
- UniProt
- P06956
- Pockets
- 14 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 57% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, D | DNA (35-mer) | dna | 33 | — | — |
| A | Protein (bacteriophage P1 cre gene) | protein | 297 | 57% helix, 0% strand | P06956 |
| B | Protein (bacteriophage P1 cre gene) | protein | 296 | 57% helix, 8% strand | P06956 |
Pockets
14 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 941 | 0.75 | 0.78 | 73 | empty |
| 2 | 279 | 0.67 | 0.83 | 32 | empty |
| 3 | 360 | 0.65 | 0.80 | 31 | empty |
| 4 | 209 | 0.57 | 0.80 | 25 | empty |
| 5 | 274 | 0.55 | 0.77 | 23 | empty |
Interfaces
6 interfaces between chains.
- C–D · 1445 Ų buried · 130 hydrogen bonds · nucleic-nucleic
- C–B · 1358 Ų buried · 28 hydrogen bonds · protein-nucleic
- D–B · 1291 Ų buried · 27 hydrogen bonds · protein-nucleic
- D–A · 1199 Ų buried · 23 hydrogen bonds · protein-nucleic
- C–A · 926 Ų buried · 19 hydrogen bonds · protein-nucleic
Compared structures
- 5CRX · Asymmetric DNA-bending in the cre-loxp site-specific recombination 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 5CRX · PDBe 5CRX · UniProt P06956
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