MolNFT v1 · #89327 · protein + DNA

TN5 transposase: 20MER outside end 2 mn complex

4DM0 · Transposase for transposon TN5: “TN5 transposase: 20MER outside end 2 mn complex”. X-ray diffraction, 1 ligand (MN), 9 pockets (best druggability 0.63). MolNFT v1 #89327 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4DM0
Type: protein + DNA
Length: 500 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Transposase for transposon TN5; DNA transferred strand; DNA non-transferred strand
EC: 3.1.-.-
UniProt: Q46731
Ligands: MN
Pockets: 9 · best druggability 0.63

Structure

x-ray diffraction · 3 distinct chains · 45% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Transposase for transposon TN5 (EC 3.1.-.-)	protein	460	45% helix, 21% strand	Q46731
B	DNA transferred strand	dna	20	—	—
C	DNA non-transferred strand	dna	20	—	—

Ligands and binding sites

MN · Manganese (II) ion · metal · 3 copies · chains A, B
EDO · 1,2-ethanediol · additive · chains A

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

Pockets

9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	485	0.63	0.77	55	empty
2	134	0.61	0.85	28	empty
3	370	0.57	0.75	40	empty
4	85	0.41	0.79	15	empty
5	121	0.36	0.73	21	MN

Interfaces

3 interfaces between chains.

A–C · 893 Å² buried · 20 hydrogen bonds · protein-nucleic
B–C · 851 Å² buried · 79 hydrogen bonds · nucleic-nucleic
A–B · 732 Å² buried · 22 hydrogen bonds · protein-nucleic

Compared structures

4DM0 · TN5 transposase: 20MER OUTSIDE END 2 MN complex · the same entry in another collection · chain A against A, TM-score 1.00
Q46731 · AlphaFold monomer V2.0 prediction for transposase for transposon TN5 (Q46731) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 Q46731
Elsewhere: RCSB PDB 4DM0 · PDBe 4DM0 · UniProt Q46731

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