MolNFT v1 · #161367 · protein

PCNA complex with CDT2 C-terminal pip-box peptide

6QC0 · Proliferating cell nuclear antigen: “PCNA complex with CDT2 C-terminal pip-box peptide”. X-ray diffraction, 5 pockets (best druggability 0.45). MolNFT v1 #161367 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6QC0
Type: protein
Length: 797 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Proliferating cell nuclear antigen; Denticleless protein homolog
UniProt: P12004, Q9NZJ0
Pockets: 5 · best druggability 0.45

Structure

x-ray diffraction · 3 distinct chains · 18% helix, 46% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Proliferating cell nuclear antigen	protein	254	19% helix, 46% strand	P12004
C, E	Proliferating cell nuclear antigen	protein	255	18% helix, 47% strand	P12004
B, D, F	Denticleless protein homolog	protein	11	0% helix, 0% strand	Q9NZJ0

Pockets

5 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	116	0.45	0.78	18	empty
2	82	0.40	0.78	16	empty
3	102	0.38	0.75	21	empty
4	90	0.37	0.76	26	empty
5	87	0.37	0.76	20	empty

Interfaces

6 interfaces between chains.

A–C · 771 Å² buried · 18 hydrogen bonds · protein-protein
A–E · 751 Å² buried · 15 hydrogen bonds · protein-protein
A–B · 747 Å² buried · 2 hydrogen bonds · protein-protein
E–F · 739 Å² buried · 8 hydrogen bonds · protein-protein
C–D · 686 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

6QC0 · PCNA complex with Cdt2 C-terminal PIP-box peptide · the same entry in another collection · chain F against F, TM-score 1.00
Q9NZJ0 · AlphaFold monomer V2.0 prediction for denticleless protein homolog (Q9NZJ0) · a predicted model of the same protein · chain F against A, TM-score 0.39

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 P12004
Every structure of UniProt Q9NZJ0
Elsewhere: RCSB PDB 6QC0 · PDBe 6QC0 · UniProt P12004 · UniProt Q9NZJ0

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