MolNFT v1 · #15946 · protein + DNA

Adenine-adenine mismatch at the polymerase active site

1NK5 · DNA primer strand: “Adenine-adenine mismatch at the polymerase active site”. X-ray diffraction, 4 ligands (GLC, FRU, MG), 9 pockets (best druggability 0.70). MolNFT v1 #15946 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 1NK5
Type: protein + DNA
Length: 608 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, 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	14	—	—
C	DNA template strand	dna	14	—	—
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 B, 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	399	0.70	0.82	46	GLC, FRU
2	289	0.69	0.84	36	empty
3	221	0.57	0.79	37	MG, SO4
4	436	0.54	0.72	35	empty
5	118	0.43	0.77	23	empty

Interfaces

3 interfaces between chains.

C–A · 1060 Å² buried · 20 hydrogen bonds · protein-nucleic
B–A · 1047 Å² buried · 21 hydrogen bonds · protein-nucleic
B–C · 590 Å² buried · 46 hydrogen bonds · nucleic-nucleic

Compared structures

1NK5 · Adenine-adenine 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 1NK5 · PDBe 1NK5 · UniProt P52026

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