Research workbench

Taq polymerase (E.C.2.7.7.7)/DNA/B-octylglucoside complex

Analyse Taq polymerase (E.C.2.7.7.7)/DNA/B-octylglucoside complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1TAU
Type: protein + DNA
Length: 809 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA (5'-D(*GP*CP*GP*AP*TP*CP*CP*G)-3'); DNA (5'-D(*CP*GP*GP*AP*TP*CP*GP*C)-3'); Protein…
EC: 2.7.7.7
UniProt: P19821
Ligands: BGL, ZN
Pockets: 11 · best druggability 0.72

Structure

x-ray diffraction · 3 distinct chains · 51% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
T	DNA (5'-D(GPCPGPAPTPCPCPG)-3')	dna	8	—	—
P	DNA (5'-D(CPGPGPAPTPCPGPC)-3')	dna	8	—	—
A	Protein (taq polymerase) (EC 2.7.7.7)	protein	793	51% helix, 13% strand	P19821

Ligands and binding sites

BGL · 2-O-octyl-beta-D-glucopyranose · ligand · chains A
ZN · Zinc ion · metal · chains A

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

Pockets

11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	260	0.72	0.87	29	empty
2	248	0.71	0.87	35	empty
3	398	0.70	0.82	35	empty
4	54	0.65	0.95	18	empty
5	194	0.64	0.84	29	empty

Interfaces

3 interfaces between chains.

T–A · 681 Å² buried · 13 hydrogen bonds · protein-nucleic
P–A · 609 Å² buried · 17 hydrogen bonds · protein-nucleic
T–P · 381 Å² buried · 36 hydrogen bonds · nucleic-nucleic

Compared structures

1TAU · Taq polymerase (E.C.2.7.7.7)/DNA/B-octylglucoside complex · the same entry in another collection · chain T against T, TM-score 1.00
P19821 · AlphaFold monomer V2.0 prediction for DNA polymerase I, thermostable (P19821) · a predicted model of the same protein · chain A against A, TM-score 0.65

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 P19821
Elsewhere: RCSB PDB 1TAU · PDBe 1TAU · UniProt P19821

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