Research workbench

Polymerase domain of polymerase-theta

Analyse Polymerase domain of polymerase-theta in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6XBU
Type: protein + DNA + RNA
Length: 620 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA polymerase theta; DNA (5'-D(P*GP*TP*CP*AP*TP*TP*G)-3'); RNA…
EC: 2.7.7.7
UniProt: O75417
Ligands: DG3
Pockets: 10 · best druggability 0.62

Structure

x-ray diffraction · 3 distinct chains · 42% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA polymerase theta (EC 2.7.7.7)	protein	605	42% helix, 13% strand	O75417
F	DNA (5'-D(PGPTPCPAPTPTP*G)-3')	dna	8	—	—
E	RNA (5'-R(PCPCPAPAPUPGP*A)-3')	rna	7	—	—

Ligands and binding sites

DG3 · 2'-3'-dideoxyguanosine-5'-triphosphate · ligand · chains A, F, E

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

Pockets

10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	393	0.62	0.78	39	DG3
2	276	0.59	0.79	32	empty
3	272	0.56	0.77	30	empty
4	276	0.55	0.76	35	empty
5	137	0.53	0.81	28	empty

Interfaces

3 interfaces between chains.

A–E · 616 Å² buried · 10 hydrogen bonds · protein-nucleic
A–F · 459 Å² buried · 5 hydrogen bonds · protein-nucleic
F–E · 331 Å² buried · 25 hydrogen bonds · nucleic-nucleic

Compared structures

6XBU · polymerase domain of polymerase-theta · the same entry in another collection · chain A against A, TM-score 1.00
O75417 · AlphaFold monomer V2.0 prediction for DNA polymerase theta (O75417) · a predicted model of the same protein · chain A against A, TM-score 0.96

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 O75417
Elsewhere: RCSB PDB 6XBU · PDBe 6XBU · UniProt O75417

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