Research workbench

Cyanophage S-2L primase-polymerase (primpol), aep domain (pp-N190)

Analyse Cyanophage S-2L primase-polymerase (primpol), aep domain (pp-N190) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6ZP9
Type: protein
Length: 370 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Primpol aep domain (pp-N190)
Ligands: CA
Pockets: 5 · best druggability 0.69

Structure

x-ray diffraction · 1 distinct chain · 31% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Primpol aep domain (pp-N190)	protein	185	31% helix, 25% strand	—

Ligands and binding sites

CA · Calcium ion · metal · 3 copies · chains A, B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	53	0.69	0.97	18	empty
2	151	0.46	0.77	24	empty
3	91	0.44	0.79	24	empty
4	111	0.42	0.77	17	empty
5	50	0.36	0.79	10	empty

Interfaces

1 interface between chains.

A–B · 656 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

6ZP9 · Cyanophage S-2L Primase-Polymerase (PrimPol), AEP domain (PP-N190) · the same entry in another collection · chain A against A, 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
Elsewhere: RCSB PDB 6ZP9 · PDBe 6ZP9

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