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The structure of a TY3 retrotransposon capsid N-terminal domain dimer

Analyse The structure of a TY3 retrotransposon capsid N-terminal domain dimer in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6R22
Type: protein
Length: 148 residues
Chains: 2
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Transposon TY3-I gag-pol polyprotein
EC: 3.4.23.-, 2.7.7.49, 2.7.7.7, 3.1.26.4
UniProt: Q7LHG5
Pockets: 3 · best druggability 0.67

Structure

electron microscopy · 1 distinct chain · 64% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Transposon TY3-I gag-pol polyprotein (EC 3.4.23.-, 2.7.7.49, 2.7.7.7, 3.1.26.4)	protein	74	64% helix, 0% strand	Q7LHG5

Pockets

3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	80	0.67	0.92	16	empty
2	82	0.67	0.91	17	empty
3	136	0.46	0.77	27	empty

Interfaces

1 interface between chains.

A–B · 252 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

6R22 · The structure of a Ty3 retrotransposon capsid N-terminal domain dimer · the same entry in another collection · chain A against A, TM-score 1.00
Q7LHG5 · AlphaFold monomer V2.0 prediction for transposon TY3-I gag-pol polyprotein (Q7LHG5) · a predicted model of the same protein · chain A against A, TM-score 0.64

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 Q7LHG5
Elsewhere: RCSB PDB 6R22 · PDBe 6R22 · UniProt Q7LHG5

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