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Crystal structure of human PCNA in complex with three peptides of P12 subunit of human polymerase delta

Analyse Crystal structure of human PCNA in complex with three peptides of P12 subunit… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6HVO
Type: protein
Length: 795 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Proliferating cell nuclear antigen; DNA polymerase delta subunit 4
UniProt: P12004, Q9HCU8
Ligands: SO4
Pockets: 4 · best druggability 0.44

Structure

x-ray diffraction · 6 distinct chains · 18% helix, 45% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Proliferating cell nuclear antigen	protein	254	18% helix, 46% strand	P12004
B	Proliferating cell nuclear antigen	protein	252	18% helix, 46% strand	P12004
C	Proliferating cell nuclear antigen	protein	252	17% helix, 48% strand	P12004
D	DNA polymerase delta subunit 4	protein	12	25% helix, 8% strand	Q9HCU8
F	DNA polymerase delta subunit 4	protein	13	23% helix, 8% strand	Q9HCU8
E	DNA polymerase delta subunit 4	protein	12	25% helix, 8% strand	Q9HCU8

Ligands and binding sites

SO4 · Sulfate ion · ion · 7 copies · chains A, E, C, B, F

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

Pockets

4 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	104	0.44	0.78	19	empty
2	93	0.34	0.74	21	empty
3	71	0.31	0.74	15	empty
4	61	0.31	0.75	16	empty

Interfaces

6 interfaces between chains.

A–B · 769 Å² buried · 11 hydrogen bonds · protein-protein
B–C · 757 Å² buried · 15 hydrogen bonds · protein-protein
A–C · 722 Å² buried · 14 hydrogen bonds · protein-protein
B–D · 706 Å² buried · 9 hydrogen bonds · protein-protein
C–F · 694 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

6HVO · Crystal structure of human PCNA in complex with three peptides of p12 subunit of human… · the same entry in another collection · chain F against F, TM-score 1.00
Q9HCU8 · AlphaFold monomer V2.0 prediction for DNA polymerase delta subunit 4 (Q9HCU8) · a predicted model of the same protein · chain D against A, TM-score 0.36

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 Q9HCU8
Elsewhere: RCSB PDB 6HVO · PDBe 6HVO · UniProt P12004 · UniProt Q9HCU8

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