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Crystal structure of a pre-cleavage MOS1 transpososome

Analyse Crystal structure of a pre-cleavage MOS1 transpososome in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4U7B
Type: protein + DNA
Length: 1,194 residues
Chains: 9
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA (25-mer); DNA (31-mer); Mariner MOS1 transposase
EC: 3.1.-.-
UniProt: Q7JQ07
Ligands: SO4
Pockets: 20 · best druggability 0.77

Structure

x-ray diffraction · 3 distinct chains · 49% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
C, E, H	DNA (25-mer)	dna	25	—	—
D, F, I	DNA (31-mer)	dna	31	—	—
A, B, G	Mariner MOS1 transposase (EC 3.1.-.-)	protein	342	49% helix, 13% strand	Q7JQ07

Ligands and binding sites

SO4 · Sulfate ion · ion · 3 copies · chains C, D, E, 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, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1151	0.77	0.79	79	empty
2	453	0.74	0.84	59	empty
3	350	0.69	0.83	40	empty
4	290	0.67	0.83	36	empty
5	247	0.65	0.83	37	empty

Interfaces

15 interfaces between chains.

A–B · 3184 Å² buried · 40 hydrogen bonds · protein-protein
D–A · 1143 Å² buried · 19 hydrogen bonds · protein-nucleic
H–I · 1139 Å² buried · 113 hydrogen bonds · nucleic-nucleic
I–G · 1138 Å² buried · 20 hydrogen bonds · protein-nucleic
C–D · 1132 Å² buried · 99 hydrogen bonds · nucleic-nucleic

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

4U7B · Crystal structure of a pre-cleavage Mos1 transpososome · the same entry in another collection · chain G against G, 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 4U7B · PDBe 4U7B · UniProt Q7JQ07

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