MolNFT v1 · #18916 · protein + DNA

Crystal structure of a wild-type cre recombinase-loxp synapse: pre-cleavage complex

1Q3U · Loxp DNA: “Crystal structure of a wild-type cre recombinase-loxp synapse: pre-cleavage complex”. X-ray diffraction, 2 ligands (MG, IOD), 20 pockets (best druggability 0.83). MolNFT v1 #18916 on GenesisL1: 3D structure, binding sites…

PDB: 1Q3U
Type: protein + DNA
Length: 1,445 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Loxp DNA; Cre recombinase
UniProt: P06956
Ligands: MG, IOD
Pockets: 20 · best druggability 0.83

Structure

x-ray diffraction · 5 distinct chains · 56% helix, 6% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
C, G	Loxp DNA	dna	37	—	—
D, H	Loxp DNA	dna	37	—	—
A	Cre recombinase	protein	332	55% helix, 5% strand	P06956
B, F	Cre recombinase	protein	322	54% helix, 8% strand	P06956
E	Cre recombinase	protein	321	57% helix, 5% strand	P06956

Ligands and binding sites

MG · Magnesium ion · metal · 10 copies · chains C, D, A, G, H, F
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

20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1056	0.83	0.85	109	MG
2	483	0.81	0.89	64	empty
3	972	0.74	0.78	89	empty
4	84	0.72	0.96	22	empty
5	912	0.72	0.77	77	empty

Interfaces

16 interfaces between chains.

E–F · 2078 Å² buried · 24 hydrogen bonds · protein-protein
A–B · 2076 Å² buried · 24 hydrogen bonds · protein-protein
A–F · 1752 Å² buried · 27 hydrogen bonds · protein-protein
B–E · 1700 Å² buried · 26 hydrogen bonds · protein-protein
G–H · 1625 Å² buried · 172 hydrogen bonds · nucleic-nucleic

Modifications

Observed in the structure: 2 modified (nucleotide modification).

Compared structures

1Q3U · Crystal structure of a wild-type Cre recombinase-loxP synapse: pre-cleavage complex · 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 1Q3U · PDBe 1Q3U · UniProt P06956

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