Research workbench

MOS1 transposase paired-end complex with left transposon end

Analyse MOS1 transposase paired-end complex with left transposon end in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4R79
Type: protein + DNA
Length: 830 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Left inverted repeat nts; Left inverted repeat ts; Left inverted repeat nts H; Mariner…
EC: 3.1.-.-
UniProt: Q7JQ07
Ligands: MN, SO4
Pockets: 20 · best druggability 0.72

Structure

x-ray diffraction · 4 distinct chains · 47% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
C, E, G	Left inverted repeat nts	dna	25	—	—
D, F	Left inverted repeat ts	dna	28	—	—
H	Left inverted repeat nts H	dna	27	—	—
A, B	Mariner MOS1 transposase (EC 3.1.-.-)	protein	336	47% helix, 14% strand	Q7JQ07

Ligands and binding sites

MN · Manganese (II) ion · metal · 2 copies · chains H, B, A
SO4 · Sulfate ion · ion · 2 copies · chains D, A, F, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

20 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	262	0.72	0.87	27	empty
2	335	0.72	0.84	32	empty
3	126	0.55	0.83	19	empty
4	118	0.53	0.83	21	empty
5	195	0.52	0.78	31	empty

Interfaces

17 interfaces between chains.

A–B · 2916 Å² buried · 37 hydrogen bonds · protein-protein
C–D · 1175 Å² buried · 130 hydrogen bonds · nucleic-nucleic
E–F · 1158 Å² buried · 122 hydrogen bonds · nucleic-nucleic
G–H · 1132 Å² buried · 122 hydrogen bonds · nucleic-nucleic
F–B · 1047 Å² buried · 13 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

4R79 · Mos1 transposase paired-end complex with left transposon end · the same entry in another collection · chain B against B, TM-score 1.00
Q7JQ07 · AlphaFold monomer V2.0 prediction for mariner MOS1 transposase (Q7JQ07) · a predicted model of the same protein · chain A against A, TM-score 0.97

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 Q7JQ07
Elsewhere: RCSB PDB 4R79 · PDBe 4R79 · UniProt Q7JQ07

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