MolNFT v1 · #59584 · protein + DNA
Cre-loxp synaptic structure
3C29 · Recombinase cre: “Cre-loxp synaptic structure”. X-ray diffraction, 20 pockets (best druggability 0.84). MolNFT v1 #59584 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3C29
- Type
- protein + DNA
- Length
- 1,425 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Recombinase cre; Loxp DNA, chain C,; Loxp DNA, chain D,F; Loxp DNA, chain E
- UniProt
- P06956
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 60% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, G, H | Recombinase cre | protein | 322 | 60% helix, 4% strand | P06956 |
| C | Loxp DNA, chain C, | dna | 35 | — | — |
| D, F | Loxp DNA, chain D,F | dna | 34 | — | — |
| E | Loxp DNA, chain E | dna | 34 | — | — |
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 | 954 | 0.84 | 0.86 | 100 | empty |
| 2 | 526 | 0.83 | 0.90 | 52 | empty |
| 3 | 982 | 0.77 | 0.79 | 94 | empty |
| 4 | 486 | 0.70 | 0.81 | 55 | empty |
| 5 | 387 | 0.69 | 0.82 | 50 | empty |
Interfaces
18 interfaces between chains.
- G–H · 2087 Ų buried · 28 hydrogen bonds · protein-protein
- A–B · 2048 Ų buried · 28 hydrogen bonds · protein-protein
- B–G · 1880 Ų buried · 36 hydrogen bonds · protein-protein
- A–H · 1861 Ų buried · 35 hydrogen bonds · protein-protein
- B–C · 1612 Ų buried · 38 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 3C29 · Cre-loxP Synaptic structure · the same entry in another collection · chain D against D, 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 3C29 · PDBe 3C29 · UniProt P06956
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