Research workbench

DNA polymerase beta I260Q ternary complex

Analyse DNA polymerase beta I260Q ternary complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6BTF
Type: protein + DNA
Length: 346 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA polymerase beta; DNA template strand; DNA primer strand; DNA downstream strand
EC: 2.7.7.7, 4.2.99.-
UniProt: P06746
Ligands: DUP, NA, MG
Pockets: 3 · best druggability 0.71

Structure

x-ray diffraction · 4 distinct chains · 52% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA polymerase beta (EC 2.7.7.7, 4.2.99.-)	protein	317	52% helix, 13% strand	P06746
T	DNA template strand	dna	14	—	—
P	DNA primer strand	dna	10	—	—
D	DNA downstream strand	dna	5	—	—

Ligands and binding sites

DUP · 2'-deoxyuridine 5'-alpha,beta-imido-triphosphate · ligand · chains A, T, P
NA · Sodium ion · metal · 3 copies · chains A, P, D
MG · Magnesium ion · metal · chains A

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

Pockets

3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	890	0.71	0.76	58	MG, DUP
2	395	0.63	0.78	27	empty
3	177	0.56	0.81	22	empty

Interfaces

5 interfaces between chains.

A–T · 737 Å² buried · 15 hydrogen bonds · protein-nucleic
T–P · 466 Å² buried · 41 hydrogen bonds · nucleic-nucleic
A–P · 377 Å² buried · 8 hydrogen bonds · protein-nucleic
A–D · 360 Å² buried · 7 hydrogen bonds · protein-nucleic
T–D · 151 Å² buried · 10 hydrogen bonds · nucleic-nucleic

Compared structures

6BTF · DNA Polymerase Beta I260Q Ternary Complex · the same entry in another collection · chain A against A, TM-score 1.00
P06746 · AlphaFold monomer V2.0 prediction for DNA polymerase beta (P06746) · a predicted model of the same protein · chain A against A, TM-score 0.95

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 P06746
Elsewhere: RCSB PDB 6BTF · PDBe 6BTF · UniProt P06746

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.