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PIF1 peptide bound to PCNA trimer

Analyse PIF1 peptide bound to PCNA trimer in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6E49
Type: protein
Length: 797 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Proliferating cell nuclear antigen; ATP-dependent DNA helicase PIF1
UniProt: P15873, P07271
Pockets: 9 · best druggability 0.60

Structure

x-ray diffraction · 4 distinct chains · 20% helix, 45% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Proliferating cell nuclear antigen	protein	255	19% helix, 47% strand	P15873
C	Proliferating cell nuclear antigen	protein	254	19% helix, 47% strand	P15873
D	ATP-dependent DNA helicase PIF1	protein	17	29% helix, 0% strand	P07271
E, F	ATP-dependent DNA helicase PIF1	protein	8	75% helix, 0% strand	P07271

Pockets

9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	92	0.60	0.88	18	empty
2	89	0.56	0.86	18	empty
3	58	0.53	0.88	17	empty
4	96	0.47	0.80	25	empty
5	79	0.41	0.79	18	empty

Interfaces

6 interfaces between chains.

B–C · 784 Å² buried · 15 hydrogen bonds · protein-protein
A–B · 768 Å² buried · 19 hydrogen bonds · protein-protein
A–C · 705 Å² buried · 13 hydrogen bonds · protein-protein
B–D · 533 Å² buried · 2 hydrogen bonds · protein-protein
C–F · 422 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

6E49 · Pif1 peptide bound to PCNA trimer · the same entry in another collection · chain F against F, TM-score 1.00
P07271 · AlphaFold monomer V2.0 prediction for ATP-dependent DNA helicase PIF1 (P07271) · a predicted model of the same protein · chain E against A, TM-score 0.90

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 P15873
Every structure of UniProt P07271
Elsewhere: RCSB PDB 6E49 · PDBe 6E49 · UniProt P15873 · UniProt P07271

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