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Crystal structure of Sylvaticin, a new secreted protein from Pythium Sylvaticum

Analyse Crystal structure of Sylvaticin, a new secreted protein from Pythium Sylvaticum in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2PR0
Type: protein
Length: 188 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 1.72
Source: Pythium sylvaticum
Molecule: sylvaticin
Ligands: NI
Pockets: 1 · best druggability 0.37

Structure

x-ray diffraction · resolution 1.72 · 1 distinct chain · 54% helix, 10% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	sylvaticin	protein	94	54% helix, 10% strand	—

Ligands and binding sites

NI · Nickel (II) ion · metal · 2 copies · chains A, B
TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains A, B

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

Pockets

1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	73	0.37	0.77	18	empty

Interfaces

1 interface between chains.

A–B · 256 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide (disulfide).

Compared structures

2PR0 · Crystal structure of sylvaticin, a new secreted protein from pythium sylvaticum · 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 2PR0 · PDBe 2PR0

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