2IPU: PFA1 Fab fragment

PFA1 Fab fragment complexed with Abeta 1-8 peptide. Determined by X-ray diffraction at 1.65 Å resolution. Released 9 Oct 2007.

Method: X-ray diffraction
Resolution: 1.65 Å
Organism: Mus musculus
Chains: 6
Atoms: 7,140
Mol. weight: 99.17 kDa
Ligands: ACM
Released: 9 Oct 2007

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

Secondary structure: helices and β-sheets

2IPU contains 37 α-helices and 94 β-strands across 6 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 G: 8 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	21
β-strand	11-12	2	22
α-helix	17	1
β-strand	18-25	8	21
β-strand	35-39	7	23
β-strand	46-52	7	23
β-strand	57-59	3	23
α-helix	61-63	3
β-strand	67-72	6	21
α-helix	73-75	3
β-strand	77-82	6	21
α-helix	84-86	3
β-strand	88-94	7	23
β-strand	103	1	23
β-strand	107-109	3	23
β-strand	110-111	2	22
α-helix	114-116	3
β-strand	117	1	24
α-helix	118-119	2
β-strand	120-124	5	25
β-strand	135-145	11	25
β-strand	146	1	24
β-strand	151-154	4	26
α-helix	155-157	3
β-strand	159	1	26
β-strand	163-171	9	25
β-strand	174-184	11	25
β-strand	194-199	6	26
α-helix	200-202	3
β-strand	204-209	6	26

Chain H: 9 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	8
β-strand	11-12	2	9
β-strand	18-25	8	8
β-strand	35-39	7	10
β-strand	46-52	7	10
β-strand	57-59	3	10
α-helix	61-63	3
β-strand	67-72	6	8
α-helix	73-75	3
β-strand	77-82	6	8
α-helix	84-86	3
β-strand	88-94	7	10
β-strand	103	1	10
β-strand	107-109	3	10
β-strand	110-111	2	9
α-helix	114-116	3
β-strand	117	1	11
α-helix	118-119	2
β-strand	120-124	5	12
α-helix	125-128	4
β-strand	135-145	11	12
β-strand	146	1	11
β-strand	151-154	4	13
α-helix	155-157	3
β-strand	163-165	3	12
α-helix	166-168	3
β-strand	169-171	3	12
β-strand	174-184	11	12
β-strand	194-199	6	13
α-helix	200-202	3
β-strand	204-209	6	13

Chain K: 9 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	14
β-strand	10-13	4	15
β-strand	19-25	7	14
β-strand	27C	1	16
β-strand	31	1	16
β-strand	33-38	6	15
β-strand	45-49	5	15
β-strand	53-54	2	15
α-helix	55	1
β-strand	62-67	6	14
β-strand	70-75	6	14
α-helix	80-82	3
β-strand	84-90	7	15
β-strand	93	1	17
α-helix	96	1
β-strand	97-98	2	15
β-strand	102-106	5	15
β-strand	110	1	18
α-helix	111-112	2
β-strand	113-117	5	19
α-helix	118-120	3
α-helix	121-125	5
β-strand	128-138	11	19
β-strand	139	1	18
β-strand	144-149	6	20
β-strand	152-154	3	20
β-strand	158-162	5	19
α-helix	163-166	4
β-strand	172-181	10	19
α-helix	182-185	4
β-strand	190-196	7	20
β-strand	204-209	6	20
α-helix	210-212	3

Chain L: 9 helices, 24 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
β-strand	93	1	4
α-helix	96	1
β-strand	97-98	2	2
β-strand	102-106	5	2
β-strand	110	1	5
α-helix	111-112	2
β-strand	113-117	5	6
α-helix	118-120	3
α-helix	121-125	5
β-strand	128-138	11	6
β-strand	139	1	5
β-strand	144-149	6	7
β-strand	152-153	2	7
β-strand	158-162	5	6
α-helix	163-166	4
β-strand	172-181	10	6
α-helix	182-187	6
β-strand	190-196	7	7
β-strand	204-209	6	7
α-helix	210-212	3

Chains P and Q: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
β-strand	3	1	17
α-helix	4-5	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
IgG2a Fab fragment Heavy Chain	K, L	protein	219	Mus musculus	A2NHM3 (AlphaFold model)
IgG2a Fab fragment Light Chain Kappa	G, H	protein	226	Mus musculus	P01863 (AlphaFold model)
abeta 1-8 peptide	P, Q	protein	8		P05067 (AlphaFold model)

Sequence of entity 1 (K, L), FASTA

>2IPU_1 IgG2a Fab fragment Heavy Chain (chains K, L)
DVLMTQTPLSLPVSLGDQASISCRSSQSIVHSNGNTYLEWYLQKPGQSPKLLIYKVSNRF
SGVPDRFSGSGSGTDFTLKISRVEAEDLGVYYCFQGSHVPLTFGAGTKLELKRADAAPTV
SIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSM
SSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Sequence of entity 2 (G, H), FASTA

>2IPU_2 IgG2a Fab fragment Light Chain Kappa (chains G, H)
QVTLKESGPGILKPSQTLSLTCSFSGFSLSTSGMGVGWIRQPSGKGLEWLAHIWWDDDRS
YNPSLKSQLTISKDAARNQVFLRITSVDTADTATYYCVRRAHTTVLGDWFAYWGQGTLVT
VSAAKTTAPSVYPLAPVCGGTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVL
QSGLYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEPRGPT

Sequence of entity 3 (P, Q), FASTA

>2IPU_3 abeta 1-8 peptide (chains P, Q)
DAEFRHDS

Ligands and cofactors

ID	Name	Formula	Copies
ACM	Acetamide	C2 H5 N O	3

Water and common crystallization additives (GOL) 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 A2NHM3 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6PXR 1.56 Å, Anti-TAU BIIB092 FAB with TAU peptide
4TPR 1.6 Å, Structure of Tau5 antibody Fab fragment
4TQE 1.6 Å, Structure of tau peptide in complex with Tau5 antibody Fab fragment
3V4U 1.64 Å, Structure of a monoclonal antibody complexed with its MHC-I antigen
3UO1 1.64 Å, Structure of a monoclonal antibody complexed with its MHC-I antigen
3V52 1.7 Å, Structure of a monoclonal antibody complexed with its MHC-I antigen
2DQU 1.7 Å, Crystal form II: high resolution crystal structure of the complex of the hydrolytic…
3UYR 1.7 Å, Structure of a monoclonal antibody complexed with its MHC-I antigen
1ZEA 1.78 Å, Structure of the anti-cholera toxin antibody Fab fragment TE33 in complex with a D-peptide
1PZ5 1.8 Å, Structural basis of peptide-carbohydrate mimicry in an antibody combining site
2DQT 1.8 Å, High resolution crystal structure of the complex of the hydrolytic antibody Fab 6D9 and…
1T2Q 1.83 Å, The Crystal Structure of an NNA7 Fab that recognizes an N-type blood group antigen

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