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O6-methyl-guanine in the polymerase template preinsertion site

Analyse O6-methyl-guanine in the polymerase template preinsertion site in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2HHX
Type: protein + DNA
Length: 593 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 5'-D(*CP*CP*TP*GP*AP*CP*TP*CP*G)-3'; 5'-D(*CP*AP*TP*(6OG)P*CP*GP*AP*GP*TP*CP*AP*GP*G)-3'…
EC: 2.7.7.7
UniProt: Q04957
Ligands: GLC, FRU, SO4
Pockets: 8 · best druggability 0.72

Structure

x-ray diffraction · 3 distinct chains · 56% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	5'-D(CPCPTPGPAPCPTPCP*G)-3'	dna	9	—	—
C	5'-D(CPAPTP(6OG)PCPGPAPGPTPCPAPGP*G)-3'	dna	10	—	—
A	DNA polymerase I (EC 2.7.7.7)	protein	574	56% helix, 13% strand	Q04957

Ligands and binding sites

GLC · alpha-D-glucopyranose · sugar · 2 copies · chains C, A
FRU · beta-D-fructofuranose · sugar · 2 copies · 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

8 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	443	0.72	0.82	45	GLC, FRU
2	528	0.65	0.77	56	SO4
3	89	0.63	0.90	19	empty
4	127	0.47	0.78	22	empty
5	82	0.40	0.78	13	empty

Interfaces

3 interfaces between chains.

C–A · 1085 Å² buried · 21 hydrogen bonds · protein-nucleic
B–A · 742 Å² buried · 20 hydrogen bonds · protein-nucleic
B–C · 435 Å² buried · 39 hydrogen bonds · nucleic-nucleic

Modifications

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

Compared structures

2HHX · O6-methyl-guanine in the polymerase template preinsertion site · the same entry in another collection · chain B against B, TM-score 1.00
Q04957 · AlphaFold monomer V2.0 prediction for DNA polymerase I (Q04957) · 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 Q04957
Elsewhere: RCSB PDB 2HHX · PDBe 2HHX · UniProt Q04957

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