MolNFT v1 · #161372 · protein

PCNA complex with CDT1 N-terminal pip-box peptide

6QCG · Proliferating cell nuclear antigen: “PCNA complex with CDT1 N-terminal pip-box peptide”. X-ray diffraction, 20 pockets (best druggability 0.84). MolNFT v1 #161372 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6QCG
Type: protein
Length: 1,578 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Proliferating cell nuclear antigen; DNA replication factor CDT1
UniProt: P12004, Q9H211
Pockets: 20 · best druggability 0.84

Structure

x-ray diffraction · 5 distinct chains · 19% helix, 47% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Proliferating cell nuclear antigen	protein	251	19% helix, 47% strand	P12004
C, D	Proliferating cell nuclear antigen	protein	250	19% helix, 48% strand	P12004
B, E	Proliferating cell nuclear antigen	protein	255	18% helix, 47% strand	P12004
F	Proliferating cell nuclear antigen	protein	257	19% helix, 46% strand	P12004
I, G, H, J, K, L	DNA replication factor CDT1	protein	10	0% helix, 0% strand	Q9H211

Pockets

20 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	735	0.84	0.87	46	empty
2	517	0.83	0.89	45	empty
3	506	0.82	0.88	45	empty
4	295	0.55	0.76	37	empty
5	279	0.52	0.75	30	empty

Interfaces

25 interfaces between chains.

A–B · 794 Å² buried · 15 hydrogen bonds · protein-protein
E–F · 767 Å² buried · 11 hydrogen bonds · protein-protein
E–D · 750 Å² buried · 10 hydrogen bonds · protein-protein
C–B · 744 Å² buried · 12 hydrogen bonds · protein-protein
A–C · 723 Å² buried · 10 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 disulfide (disulfide).

Compared structures

6QCG · PCNA complex with Cdt1 N-terminal PIP-box peptide · the same entry in another collection · chain L against L, 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 P12004
Every structure of UniProt Q9H211
Elsewhere: RCSB PDB 6QCG · PDBe 6QCG · UniProt P12004 · UniProt Q9H211

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