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Camelid heavy chain variable domains provide efficient combining sites to haptens

Analyse Camelid heavy chain variable domains provide efficient combining sites to… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1QD0
Type: protein
Length: 128 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Vhh-R2 anti-RR6 antibody
Ligands: RR6, CU
Pockets: 1 · best druggability 0.46

Structure

x-ray diffraction · 1 distinct chain · 0% helix, 46% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Vhh-R2 anti-RR6 antibody	protein	128	0% helix, 46% strand	—

Ligands and binding sites

RR6 · 3-hydroxy-7-(4-{1-[2-hydroxy-3-(2-hydroxy-5-sulfo-phenylazo)-benzyl]-2-sulfo-ethylamino}-[1,2,5]triazin-2-ylamino)-2-(2-hydroxy-5-sulfo-phenylazo)-napthalene-1,8-disulfonic acid · ligand · chains A
CU · Copper (II) ion · metal · 2 copies · chains A

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	69	0.46	0.83	15	CU

Modifications

Observed in the structure: 1 disulfide (disulfide).

Compared structures

1QD0 · Camelid heavy chain variable domains provide efficient combining sites to haptens · 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 1QD0 · PDBe 1QD0

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