2IQA: PFA2 FAB fragment, monoclinic apo form

PFA2 FAB fragment, monoclinic apo form. Determined by X-ray diffraction at 2.0 Å resolution. Released 9 Oct 2007.

Method: X-ray diffraction
Resolution: 2.0 Å
Organism: Mus musculus
Chains: 4
Atoms: 7,057
Mol. weight: 96.99 kDa
Ligands: ACM
Released: 9 Oct 2007

Explore 2IQA in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2IQA contains 32 α-helices and 91 β-strands across 4 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 A: 10 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	13
β-strand	10-13	4	14
β-strand	19-25	7	13
β-strand	27C	1	15
β-strand	31	1	15
β-strand	33-38	6	14
β-strand	45-49	5	14
β-strand	53-54	2	14
α-helix	55	1
β-strand	62-67	6	13
β-strand	70-75	6	13
α-helix	80-82	3
β-strand	84-90	7	14
α-helix	96	1
β-strand	97-98	2	14
β-strand	102-106	5	14
β-strand	110	1	16
α-helix	111-112	2
β-strand	113-117	5	17
α-helix	118-120	3
α-helix	121-125	5
β-strand	128-138	11	17
β-strand	139	1	16
β-strand	144-149	6	18
β-strand	152-154	3	18
β-strand	158-162	5	17
α-helix	163-166	4
β-strand	172-181	10	17
α-helix	182-185	4
β-strand	190-196	7	18
α-helix	203	1
β-strand	204-209	6	18
α-helix	210-212	3

Chain B: 7 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	19
β-strand	11-12	2	20
α-helix	17	1
β-strand	18-25	8	19
β-strand	35-39	7	21
β-strand	46-52	7	21
β-strand	57-59	3	21
β-strand	66-72	7	19
β-strand	77-82A	7	19
α-helix	84-86	3
β-strand	88-94	7	21
β-strand	103	1	21
β-strand	107-109	3	21
β-strand	110-111	2	20
β-strand	117	1	22
α-helix	118-119	2
β-strand	120-124	5	23
α-helix	126-128	3
β-strand	135-145	11	23
β-strand	146	1	22
β-strand	151-154	4	24
α-helix	155-157	3
β-strand	163-165	3	23
α-helix	166-168	3
β-strand	169-170	2	23
β-strand	175-184	10	23
β-strand	194-199	6	24
α-helix	200-202	3
β-strand	204-209	6	24

Chain H: 8 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	7
β-strand	11-12	2	8
β-strand	18-25	8	7
β-strand	35-39	7	9
β-strand	46-52	7	9
β-strand	57-59	3	9
α-helix	61-63	3
β-strand	67-72	6	7
β-strand	77-82	6	7
α-helix	84-86	3
β-strand	88-94	7	9
β-strand	103	1	9
β-strand	107-109	3	9
β-strand	110-111	2	8
α-helix	114-116	3
β-strand	117	1	10
α-helix	118-119	2
β-strand	120-124	5	11
α-helix	125-127	3
β-strand	135-145	11	11
β-strand	146	1	10
β-strand	151-154	4	12
α-helix	155-157	3
β-strand	159	1	12
β-strand	163-165	3	11
α-helix	166-168	3
β-strand	169-171	3	11
β-strand	174-184	11	11
β-strand	194-199	6	12
α-helix	200-202	3
β-strand	204-209	6	12

Chain L: 7 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	1
β-strand	10-13	4	2
β-strand	19-25	7	1
β-strand	27C	1	3
β-strand	31	1	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	70-75	6	1
α-helix	80-82	3
β-strand	84-90	7	2
α-helix	96	1
β-strand	97-98	2	2
β-strand	102-106	5	2
β-strand	110	1	4
β-strand	113-117	5	5
α-helix	118-120	3
α-helix	121-125	5
β-strand	128-138	11	5
β-strand	139	1	4
β-strand	143-149	7	6
β-strand	152-154	3	6
β-strand	158-162	5	5
α-helix	163-166	4
β-strand	172-181	10	5
α-helix	182-185	4
β-strand	190-197	8	6
β-strand	204-209	6	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
IgG2a Fab fragment PFA2 Kappa light chain	A, L	protein	219	Mus musculus	P01631 (AlphaFold model)
IgG2a Fab fragment PFA2 heavy chain	B, H	protein	223	Mus musculus	P01864 (AlphaFold model)

Sequence of entity 1 (A, L), FASTA

>2IQA_1 IgG2a Fab fragment PFA2 Kappa light chain (chains A, L)
DVLMTQTPLSLPVSLGDQASISCRSSQSIVHSNGNTYLEWYLQKPGQSPKLLIYKVSNRF
SGVPDRFSGSGSGTDFTLKISRVEAEDLGVYYCFQGSHVPLTFGAGTKLEIKRADAAPTV
SIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSM
SSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Sequence of entity 2 (B, H), FASTA

>2IQA_2 IgG2a Fab fragment PFA2 heavy chain (chains B, H)
QVTLKESGPGILKPSQTLSLTCSLSGFSLRTSGMGVGWIRQPSGKGLEWLAHIWWDDDKN
YNPSLKSQLTISKDTSRNQVFLKITSVDTADTATYYCVRRAHNVVLGDWFAYWGQGTLVT
VSAAKTTAPSVYPLAPVCGGTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVL
QSGLYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEPR

Ligands and cofactors

ID	Name	Formula	Copies
ACM	Acetamide	C2 H5 N O	2

Water and common crystallization additives (GOL, CL) are not listed.

Primary citation

Molecular basis for passive immunotherapy of Alzheimer's disease. Gardberg, A.S., Dice, L.T., Ou, S. et al. Proc Natl Acad Sci U S A (2007) 104:15659-15664. DOI 10.1073/pnas.0705888104 · PubMed

Other PDB entries of the same protein (UniProt P01631 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1DLF 1.45 Å, High resolution crystal structure of the fv fragment from an anti-dansyl switch variant…
2DLF 1.55 Å, High resolution crystal structure of the fv fragment from an anti-dansyl switch variant…
1N4X 1.7 Å, Structure of scFv 1696 at acidic pH
1WZ1 1.85 Å, Crystal structure of the Fv fragment complexed with dansyl-lysine
1SVZ 1.89 Å, Crystal structure of the single-chain Fv fragment 1696 in complex with the epitope…
2IPT 2.0 Å, PFA1 Fab Fragment
2HKF 2.01 Å, Crystal structure of the Complex Fab M75- Peptide
2O5X 2.05 Å, Crystal structure of 1E9 LeuH47Trp/ArgH100Trp, an engineered Diels-Alderase Fab with nM…
1BFV 2.1 Å, Monoclonal antibody fragment FV4155 from E. Coli
1CFV 2.1 Å, Monoclonal antibody fragment FV4155 from E. Coli
2HKH 2.1 Å, Crystal structure of the Fab M75
2O5Z 2.4 Å, Crystal structure of the 1E9 LeuH47Trp/ArgH100Trp Fab 5-beta-androstane-3,17-dione complex

Browse structure collections

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