Research workbench

Human polymerase delta holoenzyme conformer 3

Analyse Human polymerase delta holoenzyme conformer 3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6S1O
Type: protein + DNA
Length: 2,449 residues
Chains: 9
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA polymerase delta catalytic subunit; DNA polymerase delta subunit 2; DNA polymerase…
EC: 2.7.7.7, 3.1.11.-
UniProt: P28340, P49005, Q15054, Q9HCU8, P12004
Ligands: SF4, TTP, ZN
Pockets: 20 · best druggability 0.86

Structure

electron microscopy · 9 distinct chains · 27% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA polymerase delta catalytic subunit (EC 2.7.7.7, 3.1.11.-)	protein	1010	35% helix, 18% strand	P28340
B	DNA polymerase delta subunit 2	protein	431	20% helix, 23% strand	P49005
C	DNA polymerase delta subunit 3	protein	143	37% helix, 22% strand	Q15054
D	DNA polymerase delta subunit 4	protein	66	29% helix, 0% strand	Q9HCU8
E	Proliferating cell nuclear antigen	protein	251	18% helix, 43% strand	P12004
F	Proliferating cell nuclear antigen	protein	249	16% helix, 44% strand	P12004
G	Proliferating cell nuclear antigen	protein	249	18% helix, 45% strand	P12004
P	DNA primer	dna	23	—	—
T	DNA template	dna	27	—	—

Ligands and binding sites

SF4 · Iron/sulfur cluster · ligand · chains A
TTP · Thymidine-5'-triphosphate · ligand · chains A, P, T
ZN · Zinc ion · metal · chains A

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

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1012	0.86	0.87	96	empty
2	158	0.82	0.96	31	empty
3	524	0.79	0.86	75	empty
4	90	0.77	0.97	20	empty
5	353	0.76	0.87	35	empty

Interfaces

13 interfaces between chains.

B–C · 2650 Å² buried · 21 hydrogen bonds · protein-protein
A–B · 2108 Å² buried · 15 hydrogen bonds · protein-protein
A–T · 1193 Å² buried · 24 hydrogen bonds · protein-nucleic
P–T · 1051 Å² buried · 99 hydrogen bonds · nucleic-nucleic
A–D · 752 Å² buried · 5 hydrogen bonds · protein-protein

Modifications

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

Compared structures

6S1O · Human polymerase delta holoenzyme Conformer 3 · the same entry in another collection · chain F against F, TM-score 1.00
P12004 · AlphaFold monomer V2.0 prediction for proliferating cell nuclear antigen (P12004) · a predicted model of the same protein · chain E against A, TM-score 0.97

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 P28340
Every structure of UniProt P49005
Every structure of UniProt Q15054
Every structure of UniProt Q9HCU8
Every structure of UniProt P12004
Elsewhere: RCSB PDB 6S1O · PDBe 6S1O · UniProt P28340 · UniProt P49005 · UniProt Q15054 · UniProt Q9HCU8 · UniProt P12004

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