1BBD: IGG2A-kappa 8F5 FAB

Three dimensional structure of the FAB fragment of a neutralizing antibody to human rhinovirus serotype 2. Determined by X-ray diffraction at 2.8 Å resolution. Released 31 Jan 1994.

Method: X-ray diffraction
Resolution: 2.8 Å
Organism: Mus musculus
Chains: 2
Atoms: 3,342
Mol. weight: 48.1 kDa
Released: 31 Jan 1994

Explore 1BBD in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1BBD contains 9 α-helices and 46 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain H: 6 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	7
β-strand	10-12	3	8
β-strand	18-25	8	7
α-helix	29-31	3
β-strand	33-39	7	8
β-strand	45-52	8	8
β-strand	57-60	4	8
α-helix	62-64	3
β-strand	68-73	6	7
β-strand	78-83	6	7
α-helix	88-90	3
β-strand	92-100	9	8
β-strand	105-108	4	8
β-strand	112-116	5	8
β-strand	122	1	9
β-strand	125-129	5	10
β-strand	140-150	11	10
β-strand	151	1	9
β-strand	156-159	4	11
α-helix	160-162	3
β-strand	164	1	11
β-strand	168-170	3	10
β-strand	174-175	2	10
β-strand	180-189	10	10
α-helix	192-195	4
β-strand	199-204	6	11
α-helix	205-207	3
β-strand	209-214	6	11

Chain L: 3 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	1
β-strand	10-14	5	2
β-strand	18-24	7	1
β-strand	30-31	2	3
β-strand	36-37	2	3
β-strand	39-44	6	2
β-strand	51-55	5	2
β-strand	59-60	2	2
β-strand	69-73	5	1
β-strand	76-82	7	1
α-helix	86-88	3
β-strand	90-96	7	2
β-strand	104	1	2
β-strand	108-113	6	2
β-strand	117	1	4
β-strand	120-124	5	5
α-helix	128-132	5
β-strand	135-145	11	5
β-strand	146	1	4
β-strand	151-156	6	6
β-strand	159-161	3	6
β-strand	165-166	2	5
β-strand	169	1	5
β-strand	179-188	10	5
α-helix	189-194	6
β-strand	197-203	7	6
β-strand	211-216	6	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
IGG2A-kappa 8F5 FAB (light chain)	L	protein	220	Mus musculus	Q52L64 (AlphaFold model)
IGG2A-kappa 8F5 FAB (heavy chain)	H	protein	218	Mus musculus

Sequence of entity 1 (L), FASTA

>1BBD_1 IGG2A-KAPPA 8F5 FAB (LIGHT CHAIN) (chains L)
DIVMTQSPSSLTVTTGEKVTMTCKSSQSLLNSRTQKNYLTWYQQKPGQSPKLLIYWASTR
ESGVPDRFTGSGSGTDFTLSISGVQAEDLAVYYCQNNYNYPLTFGAGTKLELKRADAAPT
VSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYS
MSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Sequence of entity 2 (H), FASTA

>1BBD_2 IGG2A-KAPPA 8F5 FAB (HEAVY CHAIN) (chains H)
EVQLQQSGAELVRPGASVKLSCTTSGFNIKDIYIHWVKQRPEQGLEWIGRLDPANGYTKY
DPKFQGKATITVDTSSNTAYLHLSSLTSEDTAVYYCDGYYSYYDMDYWGPGTSVTVSSAK
TTAPSVYPLAPVCGDTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLY
TLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEPR

Primary citation

Three-dimensional structure of the Fab fragment of a neutralizing antibody to human rhinovirus serotype 2. Tormo, J., Stadler, E., Skern, T. et al. Protein Sci (1992) 1:1154-1161. PubMed

Other PDB entries of the same protein (UniProt Q52L64 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2R1X 1.6 Å, Crystal structure of S25-2 Fab in complex with Kdo analogues
3T77 1.74 Å, S25-2- A(2-4)KDO disaccharide complex
1JGU 1.8 Å, Structural basis for disfavored elimination reaction in catalytic antibody 1D4
1JGV 1.85 Å, Structural basis for disfavored elimination reaction in catalytic antibody 1D4
2R2H 2.0 Å, Structure of S25-2 in Complex with Ko
1A3R 2.1 Å, FAB fragment (antibody 8F5) complexed with peptide from human rhinovirus (serotype 2)…
1H3P 2.6 Å, Structural characterisation of a monoclonal antibody specific for the PRES1 region of…
5MP3 2.75 Å, Crystal structure of DC8E8 Fab in the complex with a 30-mer tau peptide at pH 6.5

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