MolNFT v1 · #169261 · protein + DNA

Cryo-EM structure of piggybac transposase synaptic complex with hairpin DNA (snhp)

6X68: “Cryo-EM structure of piggybac transposase synaptic complex with hairpin DNA (snhp)”. Electron microscopy, 2 ligands (CA, ZN), 20 pockets (best druggability 0.82). MolNFT v1 #169261 on GenesisL1: 3D structure, binding sites and…

PDB: 6X68
Type: protein + DNA
Length: 1,080 residues
Chains: 4
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Transposase; Hairpin DNA
UniProt: Q283G1
Ligands: CA, ZN
Pockets: 20 · best druggability 0.82

Structure

electron microscopy · 3 distinct chains · 38% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
C, D	Transposase	protein	478	38% helix, 15% strand	Q283G1
A	Hairpin DNA	dna	74	—	—
B	Hairpin DNA	dna	50	—	—

Ligands and binding sites

CA · Calcium ion · metal · 4 copies · chains C, B, A, D
ZN · Zinc ion · metal · 4 copies · chains C, D

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	323	0.82	0.93	62	empty
2	279	0.79	0.91	53	empty
3	194	0.74	0.91	22	empty
4	698	0.74	0.80	57	CA
5	751	0.73	0.79	63	CA

Interfaces

5 interfaces between chains.

C–A · 2404 Å² buried · 32 hydrogen bonds · protein-nucleic
D–B · 1743 Å² buried · 18 hydrogen bonds · protein-nucleic
D–A · 1703 Å² buried · 22 hydrogen bonds · protein-nucleic
C–D · 1136 Å² buried · 8 hydrogen bonds · protein-protein
C–B · 926 Å² buried · 10 hydrogen bonds · protein-nucleic

Compared structures

6X68 · Cryo-EM structure of piggyBac transposase synaptic complex with hairpin DNA (SNHP) · 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 Q283G1
Elsewhere: RCSB PDB 6X68 · PDBe 6X68 · UniProt Q283G1

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