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Ternary complex of DNA polymerase epsilon with an incoming datp

Analyse Ternary complex of DNA polymerase epsilon with an incoming datp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4M8O
Type: protein + DNA
Length: 1,152 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA polymerase epsilon catalytic subunit a; Primer DNA; Template DNA
EC: 2.7.7.7
UniProt: P21951
Ligands: TAU, DTP, MG, ZN, CL
Pockets: 13 · best druggability 0.78

Structure

x-ray diffraction · 3 distinct chains · 43% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA polymerase epsilon catalytic subunit a (EC 2.7.7.7)	protein	1126	43% helix, 23% strand	P21951
P	Primer DNA	dna	11	—	—
T	Template DNA	dna	15	—	—

Ligands and binding sites

TAU · 2-aminoethanesulfonic acid · ligand · 2 copies · chains A
DTP · 2'-deoxyadenosine 5'-triphosphate · ligand · chains A, P, T
MG · Magnesium ion · metal · chains A
ZN · Zinc ion · metal · chains A
CL · Chloride ion · ion · 2 copies · chains P, A

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

Pockets

13 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	1139	0.78	0.80	88	DTP, MG, TAU, CL
2	958	0.76	0.78	83	empty
3	306	0.72	0.86	39	empty
4	824	0.71	0.77	67	empty
5	209	0.50	0.76	40	empty

Interfaces

3 interfaces between chains.

A–T · 1381 Å² buried · 30 hydrogen bonds · protein-nucleic
A–P · 789 Å² buried · 22 hydrogen bonds · protein-nucleic
P–T · 498 Å² buried · 40 hydrogen bonds · nucleic-nucleic

Modifications

Observed in the structure: 14 modified (nucleotide modification).

Compared structures

4M8O · TERNARY COMPLEX OF DNA POLYMERASE EPSILON WITH AN INCOMING dATP · the same entry in another collection · chain A against A, TM-score 1.00
P21951 · AlphaFold monomer V2.0 prediction for DNA polymerase epsilon catalytic subunit a (P21951) · 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 P21951
Elsewhere: RCSB PDB 4M8O · PDBe 4M8O · UniProt P21951

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