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Ternary complex of hpoli with DNA and dctp

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

PDB: 2DPI
Type: protein + DNA
Length: 388 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 5'-D(*AP*GP*GP*AP*CP*CP*(DOC))-3'; 5'-D(*TP*(EDA)P*GP*GP*GP*TP*CP*CP*T)-3'; DNA…
EC: 2.7.7.7
UniProt: Q9UNA4
Ligands: DCP, MG
Pockets: 5 · best druggability 0.78

Structure

x-ray diffraction · 3 distinct chains · 45% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
P	5'-D(APGPGPAPCPCP*(DOC))-3'	dna	7	—	—
T	5'-D(TP(EDA)PGPGPGPTPCPCP*T)-3'	dna	9	—	—
A	DNA polymerase iota (EC 2.7.7.7)	protein	372	45% helix, 19% strand	Q9UNA4

Ligands and binding sites

DCP · 2'-deoxycytidine-5'-triphosphate · ligand · chains P, T, A
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

5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1157	0.78	0.80	89	MG, DCP
2	754	0.73	0.79	53	empty
3	79	0.41	0.79	16	empty
4	117	0.38	0.74	17	empty
5	64	0.29	0.74	16	empty

Interfaces

3 interfaces between chains.

T–A · 752 Å² buried · 13 hydrogen bonds · protein-nucleic
P–A · 484 Å² buried · 10 hydrogen bonds · protein-nucleic
P–T · 329 Å² buried · 24 hydrogen bonds · nucleic-nucleic

Modifications

Observed in the structure: 2 modified (nucleotide modification).

Compared structures

2DPI · Ternary complex of hPoli with DNA and dCTP · the same entry in another collection · chain P against P, TM-score 1.00
Q9UNA4 · AlphaFold monomer V2.0 prediction for DNA polymerase iota (Q9UNA4) · 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 Q9UNA4
Elsewhere: RCSB PDB 2DPI · PDBe 2DPI · UniProt Q9UNA4

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