Research workbench

DNA polymerase beta nick complex with imidodiphosphate

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

PDB: 5UGO
Type: protein + DNA
Length: 358 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA (5'-D(*CP*CP*GP*AP*CP*GP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)- 3'); DNA…
EC: 2.7.7.7, 4.2.99.-
UniProt: P06746
Ligands: 2PN, CA
Pockets: 2 · best druggability 0.74

Structure

x-ray diffraction · 4 distinct chains · 51% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
T	DNA (5'-D(CPCPGPAPCPGPGPCPGPCPAPTPCPAPGPC)- 3')	dna	16	—	—
P	DNA (5'-D(GPCPTPGPAPTPGPCPGPCP*C)-3')	dna	11	—	—
D	DNA (5'-D(PGPTPCPGP*G)-3')	dna	5	—	—
A	DNA polymerase beta (EC 2.7.7.7, 4.2.99.-)	protein	326	51% helix, 13% strand	P06746

Ligands and binding sites

2PN · Imidodiphosphoric acid · ligand · chains P, A
CA · Calcium ion · metal · 2 copies · chains P, A

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

Pockets

2 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	885	0.74	0.79	73	2PN, CA
2	210	0.58	0.81	28	empty

Interfaces

5 interfaces between chains.

T–A · 719 Å² buried · 14 hydrogen bonds · protein-nucleic
P–A · 524 Å² buried · 13 hydrogen bonds · protein-nucleic
T–P · 504 Å² buried · 44 hydrogen bonds · nucleic-nucleic
D–A · 390 Å² buried · 10 hydrogen bonds · protein-nucleic
T–D · 229 Å² buried · 18 hydrogen bonds · nucleic-nucleic

Compared structures

5UGO · DNA polymerase beta nick complex with imidodiphosphate · the same entry in another collection · chain T against T, 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 5UGO · PDBe 5UGO · UniProt P06746

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