MolNFT v1 · #183730 · protein

PCNA from chaetomium thermophilum in complex with POLD4 pip peptide

7O1F · Proliferating cell nuclear antigen: “PCNA from chaetomium thermophilum in complex with POLD4 pip peptide”. X-ray diffraction, 1 ligand (NA), 12 pockets (best druggability 0.63). MolNFT v1 #183730 on GenesisL1: 3D structure, binding…

PDB: 7O1F
Type: protein
Length: 1,525 residues
Chains: 10
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Proliferating cell nuclear antigen; Peptide fragment from POLD4
UniProt: G0SF70, G0RZ52
Ligands: NA
Pockets: 12 · best druggability 0.63

Structure

x-ray diffraction · 8 distinct chains · 19% helix, 45% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Proliferating cell nuclear antigen	protein	253	19% helix, 45% strand	G0SF70
B	Proliferating cell nuclear antigen	protein	250	20% helix, 46% strand	G0SF70
C	Proliferating cell nuclear antigen	protein	238	21% helix, 45% strand	G0SF70
D	Proliferating cell nuclear antigen	protein	254	19% helix, 45% strand	G0SF70
E	Proliferating cell nuclear antigen	protein	246	20% helix, 47% strand	G0SF70
F	Proliferating cell nuclear antigen	protein	253	19% helix, 45% strand	G0SF70
J, K, M	Peptide fragment from POLD4	protein	8	0% helix, 13% strand	G0RZ52
O	Peptide fragment from POLD4	protein	7	0% helix, 14% strand	G0RZ52

Ligands and binding sites

NA · Sodium ion · metal · 18 copies · chains A, B, C, F, D, E

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

Pockets

12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	368	0.63	0.78	48	empty
2	190	0.61	0.82	31	empty
3	211	0.60	0.81	39	empty
4	200	0.59	0.81	35	empty
5	341	0.57	0.76	45	empty

Interfaces

16 interfaces between chains.

B–D · 779 Å² buried · 3 hydrogen bonds · protein-protein
A–E · 732 Å² buried · 4 hydrogen bonds · protein-protein
D–F · 713 Å² buried · 10 hydrogen bonds · protein-protein
A–C · 708 Å² buried · 9 hydrogen bonds · protein-protein
A–B · 702 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

7O1F · PCNA from Chaetomium thermophilum in complex with PolD4 PIP peptide · the same entry in another collection · chain A against A, TM-score 1.00

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 G0SF70
Every structure of UniProt G0RZ52
Elsewhere: RCSB PDB 7O1F · PDBe 7O1F · UniProt G0SF70 · UniProt G0RZ52

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