MolNFT v2 · #155849 · protein + DNA

PolD-PCNA-DNA (form B)

6KNC · DNA polymerase II small subunit: “PolD-PCNA-DNA (form B)”. Electron microscopy at 9.3, 2 ligands (ZN, FE), 20 pockets (best druggability 0.82). MolNFT v2 #155849 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6KNC
Type: protein + DNA
Length: 2,365 residues
Chains: 7
Method: electron microscopy
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 9.3
Source: Thermococcus kodakarensis; Thermococcus kodakarensis KOD1; SYNTHETIC CONSTRUCT
Molecule: DNA polymerase II small subunit; DNA polymerase D DP2 (DNA polymerase II large) subunit…
EC: 2.7.7.7, 3.1.11.1
UniProt: Q5JET1, Q5JF32
Ligands: ZN, FE
Pockets: 20 · best druggability 0.82

Structure

electron microscopy · resolution 9.3 · 5 distinct chains · 32% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA polymerase II small subunit (EC 2.7.7.7, 3.1.11.1)	protein	450	21% helix, 24% strand	Q5JET1
B	DNA polymerase D DP2 (DNA polymerase II large) subunit	protein	1118	39% helix, 14% strand	—
C, D, E	DNA polymerase sliding clamp 1	protein	249	17% helix, 43% strand	Q5JF32
F	pri30DNA	dna	25	—	—
G	temp45DNA	dna	25	—	—

Ligands and binding sites

ZN · Zinc ion · metal · 4 copies · chains A, B
FE · Fe (III) 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	917	0.82	0.83	84	empty
2	200	0.80	0.94	30	empty
3	541	0.80	0.86	70	empty
4	96	0.78	0.98	26	empty
5	610	0.78	0.84	64	empty

Interfaces

17 interfaces between chains.

A–B · 1880 Å² buried · 14 hydrogen bonds · protein-protein
B–E · 1332 Å² buried · 11 hydrogen bonds · protein-protein
F–G · 1190 Å² buried · 141 hydrogen bonds · nucleic-nucleic
C–D · 833 Å² buried · 15 hydrogen bonds · protein-protein
C–E · 781 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

6KNC · Pold-PCNA-DNA (form B) · the same entry in another collection · chain G against G, TM-score 1.00
Q5JF32 · AlphaFold monomer V2.0 prediction for DNA polymerase sliding clamp 1 (Q5JF32) · a predicted model of the same protein · chain C against A, TM-score 0.95

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 Q5JET1
Every structure of UniProt Q5JF32
Elsewhere: RCSB PDB 6KNC · PDBe 6KNC · UniProt Q5JET1 · UniProt Q5JF32

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