MolNFT v1 · #121216 · protein + DNA

Crystal structure of the MOS1 strand transfer complex

5HOO · Mariner MOS1 transposase: “Crystal structure of the MOS1 strand transfer complex”. X-ray diffraction, 1 ligand (MG), 20 pockets (best druggability 0.78). MolNFT v1 #121216 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 5HOO
Type: protein + DNA
Length: 813 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Mariner MOS1 transposase; MOS1 ir DNA nts; MOS1 ir ts joined to target DNA,MOS1 ir ts…
EC: 3.1.-.-
UniProt: Q7JQ07
Ligands: MG
Pockets: 20 · best druggability 0.78

Structure

x-ray diffraction · 5 distinct chains · 51% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Mariner MOS1 transposase (EC 3.1.-.-)	protein	335	52% helix, 13% strand	Q7JQ07
B	Mariner MOS1 transposase (EC 3.1.-.-)	protein	336	51% helix, 13% strand	Q7JQ07
C, E	MOS1 ir DNA nts	dna	25	—	—
D, F	MOS1 ir ts joined to target DNA,MOS1 ir ts joined to target DNA	dna	36	—	—
G, H	Target DNA	dna	10	—	—

Ligands and binding sites

MG · Magnesium ion · metal · 2 copies · chains A, F, G, B, H

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

Pockets

20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	557	0.78	0.85	54	empty
2	246	0.73	0.88	39	empty
3	102	0.65	0.90	19	empty
4	269	0.60	0.80	32	empty
5	143	0.58	0.84	20	empty

Interfaces

20 interfaces between chains.

A–B · 3102 Å² buried · 39 hydrogen bonds · protein-protein
B–F · 1462 Å² buried · 25 hydrogen bonds · protein-nucleic
A–D · 1444 Å² buried · 24 hydrogen bonds · protein-nucleic
C–D · 1150 Å² buried · 101 hydrogen bonds · nucleic-nucleic
E–F · 1115 Å² buried · 94 hydrogen bonds · nucleic-nucleic

Modifications

Observed in the structure: 1 disulfide (disulfide).

Compared structures

5HOO · Crystal structure of the Mos1 Strand Transfer Complex · the same entry in another collection · chain H against H, TM-score 1.00
Q7JQ07 · AlphaFold monomer V2.0 prediction for mariner MOS1 transposase (Q7JQ07) · a predicted model of the same protein · chain B against A, TM-score 0.98

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 5HOO · PDBe 5HOO · UniProt Q7JQ07

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