Research workbench
Cre recombinase-DNA transition state
Analyse Cre recombinase-DNA transition state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3MGV
- Type
- protein + DNA
- Length
- 1,428 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Recombinase cre; DNA (5'-D(*TP*AP*TP*AP*AP*CP*TP*TP*CP*GP*TP*AP*TP*AP*G)- 3'); DNA (5'…
- UniProt
- P06956
- Ligands
- VO4
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 60% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Recombinase cre | protein | 322 | 60% helix, 4% strand | P06956 |
| E, G, I, L | DNA (5'-D(*TP*AP*TP*AP*AP*CP*TP*TP*CP*GP*TP*AP*TP*AP*G)- 3') | dna | 15 | — | — |
| F, H, K, M | DNA (5'- D(*CP*AP*TP*AP*TP*GP*CP*TP*AP*TP*AP*CP*GP*AP*AP*GP*TP*TP*AP*T)-3') | dna | 20 | — | — |
Ligands and binding sites
- VO4 · Vanadate ion · ion · 2 copies · chains B, E, F, D, I, K
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 371 | 0.83 | 0.92 | 42 | empty |
| 2 | 1012 | 0.82 | 0.83 | 99 | empty |
| 3 | 973 | 0.77 | 0.79 | 107 | empty |
| 4 | 526 | 0.70 | 0.80 | 50 | empty |
| 5 | 431 | 0.70 | 0.81 | 56 | empty |
Interfaces
31 interfaces between chains.
- C–D · 2136 Ų buried · 30 hydrogen bonds · protein-protein
- A–B · 2110 Ų buried · 28 hydrogen bonds · protein-protein
- B–C · 1834 Ų buried · 31 hydrogen bonds · protein-protein
- A–D · 1825 Ų buried · 35 hydrogen bonds · protein-protein
- D–M · 1504 Ų buried · 37 hydrogen bonds · protein-nucleic
Compared structures
- 3MGV · Cre recombinase-DNA transition state · 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 3MGV · PDBe 3MGV · UniProt P06956
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