1A3R: FAB fragment

FAB fragment (antibody 8F5) complexed with peptide from human rhinovirus (serotype 2) viral capsid protein VP2 (residues 156-170). Determined by X-ray diffraction at 2.1 Å resolution. Released 29 Apr 1998.

Method: X-ray diffraction
Resolution: 2.1 Å
Organisms: Mus musculus, Human rhinovirus 2
Chains: 3
Atoms: 3,669
Mol. weight: 49.72 kDa
Released: 29 Apr 1998

Explore 1A3R in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1A3R contains 21 α-helices and 45 β-strands across 3 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: 10 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	5-6	2	7
α-helix	7-9	3
β-strand	10-12	3	8
β-strand	18-23	6	7
α-helix	29-31	3
β-strand	33-39	7	8
β-strand	45-51	7	8
β-strand	57-59	3	8
α-helix	61-63	3
β-strand	67-72	6	7
α-helix	73-75	3
β-strand	77-82	6	7
α-helix	84-86	3
β-strand	88-96	9	8
β-strand	100A-103	4	8
β-strand	107-111	5	8
α-helix	114-116	3
β-strand	117	1	9
β-strand	120-124	5	10
α-helix	125-127	3
β-strand	137-147	11	10
β-strand	148	1	9
β-strand	153-157	4	11
α-helix	162-164	3
β-strand	166	1	11
β-strand	171-173	3	10
α-helix	174-176	3
β-strand	177-178	2	10
β-strand	185-194	10	10
β-strand	206-212	6	11
α-helix	213-215	3
β-strand	217-222	6	11

Chain L: 10 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	1
β-strand	10-14	5	2
β-strand	18-25	8	1
β-strand	27C-27D	2	3
β-strand	30-31	2	3
β-strand	33-38	6	2
β-strand	45-49	5	2
β-strand	53-54	2	2
α-helix	55	1
β-strand	62-67	6	1
β-strand	70-76	7	1
α-helix	80-82	3
β-strand	84-90	7	2
α-helix	97	1
β-strand	98	1	2
α-helix	99	1
β-strand	102-107	6	2
β-strand	111	1	4
α-helix	112-113	2
β-strand	114-118	5	5
α-helix	119-121	3
α-helix	122-126	5
β-strand	129-139	11	5
β-strand	140	1	4
β-strand	144-150	7	6
β-strand	153-155	3	6
β-strand	159-163	5	5
α-helix	164-167	4
β-strand	173-182	10	5
α-helix	183-187	5
β-strand	191-198	8	6
α-helix	204	1
β-strand	205-210	6	6

Chain P: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	164-166	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
IGG2A 8F5 FAB (light chain)	L	protein	220	Mus musculus	Q52L64 (AlphaFold model)
IGG2A 8F5 FAB (heavy chain)	H	protein	218	Mus musculus	Q505N9 (AlphaFold model)
Human rhinovirus capsid protein VP2	P	protein	16	Human rhinovirus 2	P04936 (AlphaFold model)

Sequence of entity 1 (L), FASTA

>1A3R_1 IGG2A 8F5 FAB (LIGHT CHAIN) (chains L)
DIVMTQSPSSLTVTTGEKVTMTCKSSQSLLNSRTQKNYLTWYQQKPGQSPKLLIYWASTR
ESGVPDRFTGSGSGTDFTLSISGVQAEDLAVYYCQNNYNYPLTFGAGTKLELKRADAAPT
VSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYS
MSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Sequence of entity 2 (H), FASTA

>1A3R_2 IGG2A 8F5 FAB (HEAVY CHAIN) (chains H)
EVQLQQSGAELVRPGASVKLSCTTSGFNIKDIYIHWVKQRPEQGLEWIGRLDPANGYTKY
DPKFQGKATITVDTSSNTAYLHLSSLTSEDTAVYYCDGYYSYYDMDYWGPGTSVTVSSAK
TTAPSVYPLAPVCGDTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLY
TLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEPR

Sequence of entity 3 (P), FASTA

>1A3R_3 HUMAN RHINOVIRUS CAPSID PROTEIN VP2 (chains P)
VKAETRLNPDLQPTEX

Primary citation

Crystal structure of a human rhinovirus neutralizing antibody complexed with a peptide derived from viral capsid protein VP2. Tormo, J., Blaas, D., Parry, N.R. et al. EMBO J (1994) 13:2247-2256. 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
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
1BBD 2.8 Å, Three dimensional structure of the FAB fragment of a neutralizing antibody to human…

Browse structure collections

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