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Ternary complex of DNA polymerase delta

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

PDB: 3IAY
Type: protein + DNA
Length: 913 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 5'-D(*AP*TP*CP*CP*TP*CP*CP*CP*CP*TP*AP*(DOC))-3'…
EC: 2.7.7.7
UniProt: P15436
Ligands: DCP, CA
Pockets: 8 · best druggability 0.82

Structure

x-ray diffraction · 3 distinct chains · 40% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
P	5'-D(APTPCPCPTPCPCPCPCPTPAP(DOC))-3'	dna	12	—	—
T	5'-D(TPAPAPGPGPTPAPGPGPGPGPAPGPGPAPT)-3'	dna	16	—	—
A	DNA polymerase delta catalytic subunit (EC 2.7.7.7)	protein	885	40% helix, 22% strand	P15436

Ligands and binding sites

DCP · 2'-deoxycytidine-5'-triphosphate · ligand · chains P, T, A
CA · Calcium ion · metal · 5 copies · chains T, A, P
ACT · Acetate ion · additive · 2 copies · chains T, A

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

Pockets

8 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	825	0.82	0.84	97	DCP, CA
2	304	0.80	0.91	38	empty
3	221	0.49	0.75	41	empty
4	167	0.45	0.75	24	CA
5	84	0.35	0.75	20	empty

Interfaces

3 interfaces between chains.

T–A · 1581 Å² buried · 25 hydrogen bonds · protein-nucleic
P–A · 752 Å² buried · 19 hydrogen bonds · protein-nucleic
P–T · 528 Å² buried · 46 hydrogen bonds · nucleic-nucleic

Modifications

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

Compared structures

3IAY · Ternary complex of DNA polymerase delta · the same entry in another collection · chain A against A, TM-score 1.00
P15436 · AlphaFold monomer V2.0 prediction for DNA polymerase delta catalytic subunit (P15436) · 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 P15436
Elsewhere: RCSB PDB 3IAY · PDBe 3IAY · UniProt P15436

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