MolNFT v2 · #226026 · protein

Crystal structure of the C. difficile toxin A CROPs domain fragment 2592-2710 bound to H5.2 nanobody

8YVJ · H5.2 nanobody (VHH): “Crystal structure of the C. difficile toxin A CROPs domain fragment 2592-2710 bound to H5.2 nanobody”. X-ray diffraction at 1.65, 1 ligand (PO4). MolNFT v2 #226026 on GenesisL1: 3D structure, binding sites and…

PDB: 8YVJ
Type: protein
Length: 247 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 1.65
Source: Camelus dromedarius; Clostridioides difficile 342
Molecule: H5.2 nanobody (VHH); Toxin A
EC: 3.4.22.-
UniProt: P16154
Ligands: PO4

Structure

x-ray diffraction · resolution 1.65 · 2 distinct chains · 1% helix, 49% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	H5.2 nanobody (VHH)	protein	129	2% helix, 50% strand	—
B	Toxin A (EC 3.4.22.-)	protein	118	0% helix, 48% strand	P16154

Ligands and binding sites

PO4 · Phosphate ion · ion · chains A
EDO · 1,2-ethanediol · additive · chains A

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

Interfaces

1 interface between chains.

A–B · 656 Å² buried · 19 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 disulfide (disulfide).

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 P16154
Elsewhere: RCSB PDB 8YVJ · PDBe 8YVJ · UniProt P16154

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