MolNFT v1 · #154818 · protein + DNA

Pold-PCNA-DNA (form a)

6KNB · DNA polymerase II small subunit: “Pold-PCNA-DNA (form a)”. Electron microscopy, 2 ligands (ZN, FE), 20 pockets (best druggability 0.86). MolNFT v1 #154818 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6KNB
Type: protein + DNA
Length: 2,367 residues
Chains: 7
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
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 0.86

Structure

electron microscopy · 5 distinct chains · 33% helix, 17% 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	22% helix, 18% strand	Q5JET1
B	DNA polymerase D DP2 (DNA polymerase II large) subunit	protein	1120	41% helix, 11% strand	—
C, D, E	DNA polymerase sliding clamp 1	protein	249	17% helix, 45% strand	Q5JF32
F	PRI25DNA	dna	25	—	—
G	TEMP35DNA	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	1049	0.86	0.87	126	empty
2	746	0.84	0.87	116	empty
3	400	0.83	0.91	70	empty
4	792	0.81	0.85	105	empty
5	497	0.81	0.88	78	empty

Interfaces

16 interfaces between chains.

A–B · 1745 Å² buried · 12 hydrogen bonds · protein-protein
F–G · 1165 Å² buried · 93 hydrogen bonds · nucleic-nucleic
C–D · 729 Å² buried · 15 hydrogen bonds · protein-protein
D–E · 704 Å² buried · 19 hydrogen bonds · protein-protein
C–E · 647 Å² buried · 13 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

6KNB · PolD-PCNA-DNA (form A) · the same entry in another collection · chain D against D, 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 6KNB · PDBe 6KNB · UniProt Q5JET1 · UniProt Q5JF32

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.