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Crystal structure of hpcna bound to residues 452-466 of the DNA polymerase-delta-P66 subunit

Analyse Crystal structure of hpcna bound to residues 452-466 of the DNA… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1U76
Type: protein
Length: 795 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Proliferating cell nuclear antigen; Kanrqvsitgffqrk peptide from DNA polymerase delta…
UniProt: P12004, Q15054
Pockets: 5 · best druggability 0.34

Structure

x-ray diffraction · 5 distinct chains · 18% helix, 45% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Proliferating cell nuclear antigen	protein	253	18% helix, 45% strand	P12004
B	Kanrqvsitgffqrk peptide from DNA polymerase delta subunit 3	protein	12	25% helix, 17% strand	Q15054
C	Proliferating cell nuclear antigen	protein	251	18% helix, 46% strand	P12004
D, F	Kanrqvsitgffqrk peptide from DNA polymerase delta subunit 3	protein	13	23% helix, 23% strand	Q15054
E	Proliferating cell nuclear antigen	protein	253	18% helix, 45% strand	P12004

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	74	0.34	0.76	18	empty
2	54	0.31	0.76	14	empty
3	58	0.30	0.75	12	empty
4	53	0.26	0.74	19	empty
5	51	0.26	0.74	16	empty

Interfaces

6 interfaces between chains.

C–D · 820 Å² buried · 11 hydrogen bonds · protein-protein
E–F · 801 Å² buried · 9 hydrogen bonds · protein-protein
A–C · 756 Å² buried · 13 hydrogen bonds · protein-protein
A–B · 751 Å² buried · 8 hydrogen bonds · protein-protein
A–E · 748 Å² buried · 13 hydrogen bonds · protein-protein

Compared structures

1U76 · Crystal structure of hPCNA bound to residues 452-466 of the DNA polymerase-delta-p66… · the same entry in another collection · chain F against F, TM-score 1.00
Q15054 · AlphaFold monomer V2.0 prediction for DNA polymerase delta subunit 3 (Q15054) · a predicted model of the same protein · chain B against A, TM-score 0.35

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 Q15054
Elsewhere: RCSB PDB 1U76 · PDBe 1U76 · UniProt P12004 · UniProt Q15054

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