MolNFT v1 · #1756 · protein

Three dimensional structure of the Fab fragment of a neutralizing antibody to human rhinovirus serotype 2

1BBD · IGG2A-kappa 8F5 Fab (light chain): “Three dimensional structure of the Fab fragment of a neutralizing antibody to human rhinovirus serotype 2”. X-ray diffraction, 1 ligand (SO4), 3 pockets (best druggability 0.63). MolNFT v1 #1756…

PDB: 1BBD
Type: protein
Length: 432 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: IGG2A-kappa 8F5 Fab (light chain); IGG2A-kappa 8F5 Fab (heavy chain)
Ligands: SO4
Pockets: 3 · best druggability 0.63

Structure

x-ray diffraction · 2 distinct chains · 8% helix, 52% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L	IGG2A-kappa 8F5 Fab (light chain)	protein	219	6% helix, 51% strand	—
H	IGG2A-kappa 8F5 Fab (heavy chain)	protein	213	9% helix, 54% strand	—

Ligands and binding sites

SO4 · Sulfate ion · ion · chains H

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

Pockets

3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	642	0.63	0.74	62	empty
2	238	0.61	0.80	24	SO4
3	52	0.32	0.77	14	empty

Interfaces

1 interface between chains.

L–H · 1881 Å² buried · 20 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

1BBD · Three dimensional structure of the Fab fragment of a neutralizing antibody to human… · the same entry in another collection · chain L against L, 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 1BBD · PDBe 1BBD

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