Research workbench
Cre RECOMBINASE/DNA complex reaction intermediate I
Analyse Cre RECOMBINASE/DNA complex reaction intermediate I in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1CRX
- Type
- protein + DNA
- Length
- 712 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'- D(*TP*AP*TP*AP*AP*CP*TP*TP*CP*GP*TP*AP*TP*AP*G)-3'); DNA (5'…
- UniProt
- P06956
- Ligands
- PO4
- Pockets
- 12 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 59% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | DNA (5'- D(*TP*AP*TP*AP*AP*CP*TP*TP*CP*GP*TP*AP*TP*AP*G)-3') | dna | 15 | — | — |
| D, F | DNA (5'- D(*AP*TP*AP*TP*GP*CP*TP*AP*TP*AP*CP*GP*AP*AP*GP*TP*TP*AP*T) -3') | dna | 19 | — | — |
| E | DNA (5'- D(P*AP*TP*AP*AP*CP*TP*TP*CP*GP*TP*AP*TP*AP*GP*C)-3') | dna | 15 | — | — |
| A, B | Cre recombinase | protein | 322 | 59% helix, 6% strand | P06956 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · chains C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 745 | 0.84 | 0.88 | 80 | empty |
| 2 | 340 | 0.74 | 0.86 | 37 | empty |
| 3 | 223 | 0.61 | 0.81 | 27 | empty |
| 4 | 313 | 0.59 | 0.77 | 31 | empty |
| 5 | 121 | 0.57 | 0.84 | 19 | empty |
Interfaces
12 interfaces between chains.
- A–B · 1747 Ų buried · 34 hydrogen bonds · protein-protein
- F–B · 1382 Ų buried · 26 hydrogen bonds · protein-nucleic
- C–B · 1312 Ų buried · 24 hydrogen bonds · protein-nucleic
- E–A · 1303 Ų buried · 28 hydrogen bonds · protein-nucleic
- D–A · 1092 Ų buried · 18 hydrogen bonds · protein-nucleic
Compared structures
- 1CRX · Cre RECOMBINASE/DNA complex reaction intermediate I · 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 1CRX · PDBe 1CRX · UniProt P06956
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