MolNFT v1 · #78946 · protein

Crystal structure of a line-1 type transposase domain-containing protein 1 (L1TD1) from homo sapiens at 2.73 a resolution

3SOO: “Crystal structure of a line-1 type transposase domain-containing protein 1 (L1TD1) from homo sapiens at 2.73…”. X-ray diffraction, 2 ligands (SO4, CL), 2 pockets (best druggability 0.69). MolNFT v1 #78946 on GenesisL1: 3D structure…

PDB: 3SOO
Type: protein
Length: 260 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Line-1 type transposase domain-containing protein 1
UniProt: Q5T7N2
Ligands: SO4, CL
Pockets: 2 · best druggability 0.69

Structure

x-ray diffraction · 2 distinct chains · 28% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Line-1 type transposase domain-containing protein 1	protein	87	29% helix, 14% strand	Q5T7N2
C	Line-1 type transposase domain-containing protein 1	protein	86	28% helix, 26% strand	Q5T7N2

Ligands and binding sites

SO4 · Sulfate ion · ion · 8 copies · chains A, B, C
CL · Chloride ion · ion · chains C

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	600	0.69	0.78	57	SO4
2	132	0.45	0.77	21	empty

Interfaces

3 interfaces between chains.

B–C · 2579 Å² buried · 32 hydrogen bonds · protein-protein
A–B · 708 Å² buried · 7 hydrogen bonds · protein-protein
A–C · 379 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 36 modified (methylation, engineered).

Compared structures

3SOO · Crystal structure of a LINE-1 type transposase domain-containing protein 1 (L1TD1) from… · the same entry in another collection · chain A against A, TM-score 1.00
Q5T7N2 · AlphaFold monomer V2.0 prediction for line-1 type transposase domain- containing protein… · a predicted model of the same protein · chain A against A, TM-score 0.54

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 Q5T7N2
Elsewhere: RCSB PDB 3SOO · PDBe 3SOO · UniProt Q5T7N2

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