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Crystal structure of E.coli Pol II-normal DNA-dGTP ternary complex

Analyse Crystal structure of E.coli Pol II-normal DNA-dGTP ternary complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3MAQ
Type: protein + DNA
Length: 806 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 2.4
Source: Escherichia coli; SYNTHETIC CONSTRUCT
Molecule: DNA polymerase II; DNA (5'-D(*TP*AP*CP*GP*TP*AP*CP*GP*CP*TP*AP*GP*GP*CP*AP*CP*A)-3'); DNA…
EC: 2.7.7.7
UniProt: P21189
Ligands: DGT, MG
Pockets: 8 · best druggability 0.80

Structure

x-ray diffraction · resolution 2.4 · 3 distinct chains · 41% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA polymerase II (EC 2.7.7.7)	protein	776	41% helix, 25% strand	P21189
T	DNA (5'-D(TPAPCPGPTPAPCPGPCPTPAPGPGPCPAPCP*A)-3')	dna	17	—	—
P	DNA (5'-D(GPTPGPCPCPTPAPGPCPGPTPAP*(DOC))-3')	dna	13	—	—

Ligands and binding sites

DGT · 2'-deoxyguanosine-5'-triphosphate · ligand · chains A, T, P
MG · Magnesium ion · metal · 2 copies · chains A, P

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

Pockets

8 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	153	0.80	0.96	30	empty
2	959	0.78	0.80	70	empty
3	329	0.63	0.79	37	DGT, MG
4	134	0.52	0.81	23	empty
5	103	0.52	0.82	21	empty

Interfaces

3 interfaces between chains.

A–T · 1395 Å² buried · 14 hydrogen bonds · protein-nucleic
A–P · 787 Å² buried · 17 hydrogen bonds · protein-nucleic
T–P · 610 Å² buried · 56 hydrogen bonds · nucleic-nucleic

Modifications

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

Compared structures

3MAQ · Crystal structure of E.COLI pol II-normal DNA-dgtp ternary complex · the same entry in another collection · chain A against A, TM-score 1.00
P21189 · AlphaFold monomer V2.0 prediction for DNA polymerase II (P21189) · a predicted model of the same protein · chain A against A, TM-score 1.00

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 P21189
Elsewhere: RCSB PDB 3MAQ · PDBe 3MAQ · UniProt P21189

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