Research workbench

DNA polymerase X from thermus thermophilus HB8 complexed with ca-dgtp

Analyse DNA polymerase X from thermus thermophilus HB8 complexed with ca-dgtp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3AU2
Type: protein
Length: 575 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA polymerase beta family (X family)
EC: 2.7.7.7
UniProt: Q5SJ64
Ligands: DGT, CA, ZN, CL
Pockets: 5 · best druggability 0.69

Structure

x-ray diffraction · 1 distinct chain · 49% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA polymerase beta family (X family) (EC 2.7.7.7)	protein	575	49% helix, 15% strand	Q5SJ64

Ligands and binding sites

DGT · 2'-deoxyguanosine-5'-triphosphate · ligand · chains A
CA · Calcium ion · metal · 4 copies · chains A
ZN · Zinc ion · metal · 3 copies · chains A
CL · Chloride ion · ion · chains A

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

Pockets

5 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	795	0.69	0.75	74	DGT, CA
2	59	0.51	0.86	16	empty
3	85	0.35	0.75	23	empty
4	53	0.29	0.75	10	empty
5	56	0.29	0.75	16	ZN

Compared structures

3AU2 · DNA polymerase X from Thermus thermophilus HB8 complexed with Ca-dGTP · the same entry in another collection · chain A against A, 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 Q5SJ64
Elsewhere: RCSB PDB 3AU2 · PDBe 3AU2 · UniProt Q5SJ64

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