MolNFT v1 · #151705 · protein

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

6HVO · Proliferating cell nuclear antigen: “Crystal structure of human PCNA in complex with three peptides of P12 subunit of human polymerase delta”. X-ray diffraction, 1 ligand (SO4), 4 pockets (best druggability 0.44). MolNFT v1 #151705…

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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