MolNFT v1 · #15947 · protein + DNA

Cytosine-cytosine mismatch at the polymerase active site

1NK6 · DNA primer strand: “Cytosine-cytosine mismatch at the polymerase active site”. X-ray diffraction, 3 ligands (GLC, FRU, SO4), 12 pockets (best druggability 0.75). MolNFT v1 #15947 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 1NK6
Type: protein + DNA
Length: 598 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA primer strand; DNA template strand; DNA polymerase I
EC: 2.7.7.7
UniProt: P52026
Ligands: GLC, FRU, SO4
Pockets: 12 · 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	9	—	—
C	DNA template strand	dna	9	—	—
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 · 2 copies · chains A
FRU · beta-D-fructofuranose · sugar · 2 copies · 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

12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	102	0.75	0.96	27	empty
2	126	0.73	0.94	17	empty
3	354	0.68	0.81	43	GLC, FRU
4	295	0.59	0.78	39	SO4
5	489	0.58	0.73	39	empty

Interfaces

3 interfaces between chains.

B–A · 867 Å² buried · 21 hydrogen bonds · protein-nucleic
C–A · 810 Å² buried · 12 hydrogen bonds · protein-nucleic
B–C · 378 Å² buried · 30 hydrogen bonds · nucleic-nucleic

Compared structures

1NK6 · Cytosine-cytosine mismatch at the polymerase active site · 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 1NK6 · PDBe 1NK6 · UniProt P52026

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