Research workbench

Extension of an adenine-8OXOGUANINE mismatch

Analyse Extension of an adenine-8OXOGUANINE mismatch in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1U4B
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 0.75

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 · 4 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, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	149	0.75	0.94	20	empty
2	816	0.69	0.76	67	SO4, MG
3	354	0.68	0.81	42	GLC, FRU
4	221	0.60	0.81	21	empty
5	52	0.55	0.89	13	empty

Interfaces

3 interfaces between chains.

C–A · 1025 Å² buried · 21 hydrogen bonds · protein-nucleic
B–A · 768 Å² buried · 18 hydrogen bonds · protein-nucleic
B–C · 450 Å² buried · 30 hydrogen bonds · nucleic-nucleic

Modifications

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

Compared structures

1U4B · Extension of an adenine-8oxoguanine mismatch · 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 1U4B · PDBe 1U4B · UniProt P52026

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