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Crystal structure of lhk-exo in complex with 5-phosphorylated oligothymidine (DT)4

Analyse Crystal structure of lhk-exo in complex with 5-phosphorylated oligothymidine… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3SZ5
Type: protein + DNA
Length: 198 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Exonuclease; 5'-D(P*TP*TP*TP*T)-3'
UniProt: C1D7P6
Ligands: MG
Pockets: 3 · best druggability 0.55

Structure

x-ray diffraction · 2 distinct chains · 56% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Exonuclease	protein	194	56% helix, 16% strand	C1D7P6
B	5'-D(PTPTPTPT)-3'	dna	4	—	—

Ligands and binding sites

MG · Magnesium ion · metal · 2 copies · chains A, B

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

Pockets

3 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	161	0.55	0.81	29	empty
2	52	0.43	0.83	16	empty
3	82	0.37	0.77	16	empty

Interfaces

1 interface between chains.

A–B · 649 Å² buried · 14 hydrogen bonds · protein-nucleic

Compared structures

3SZ5 · Crystal Structure of LHK-Exo in complex with 5-phosphorylated oligothymidine (dT)4 · the same entry in another collection · chain A against A, TM-score 1.00

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Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt C1D7P6
Elsewhere: RCSB PDB 3SZ5 · PDBe 3SZ5 · UniProt C1D7P6

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