Research workbench

Extension of a cytosine-8-oxoguanine base pair

Analyse Extension of a cytosine-8-oxoguanine base pair in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1U48
Type: protein + DNA
Length: 603 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA primer strand; DNA template strand with 8-oxoguanine; DNA polymerase I
EC: 2.7.7.7
UniProt: P52026
Ligands: GLC, FRU, MG, SO4
Pockets: 9 · best druggability 0.70

Structure

x-ray diffraction · 3 distinct chains · 55% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	DNA primer strand	dna	10	—	—
C	DNA template strand with 8-oxoguanine	dna	13	—	—
A	DNA polymerase I (EC 2.7.7.7)	protein	580	55% helix, 13% strand	P52026

Ligands and binding sites

GLC · alpha-D-glucopyranose · sugar · chains A
FRU · beta-D-fructofuranose · sugar · chains A
MG · Magnesium ion · metal · chains A
SO4 · Sulfate ion · ion · 3 copies · chains A

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

Pockets

9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	295	0.70	0.85	33	empty
2	355	0.68	0.81	43	GLC, FRU
3	358	0.65	0.80	41	SO4, MG
4	466	0.56	0.73	33	empty
5	121	0.47	0.79	22	empty

Interfaces

3 interfaces between chains.

C–A · 1059 Å² buried · 17 hydrogen bonds · protein-nucleic
B–A · 841 Å² buried · 22 hydrogen bonds · protein-nucleic
B–C · 482 Å² buried · 41 hydrogen bonds · nucleic-nucleic

Modifications

Observed in the structure: 1 modified (nucleotide modification).

Compared structures

1U48 · Extension of a cytosine-8-oxoguanine base pair · the same entry in another collection · chain B against B, TM-score 1.00
P52026 · AlphaFold monomer V2.0 prediction for DNA polymerase I (P52026) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 P52026
Elsewhere: RCSB PDB 1U48 · PDBe 1U48 · UniProt P52026

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