5MYK: Pyroglutamate-Abeta-specific Fab c#17

Structure of Pyroglutamate-Abeta-specific Fab c#17 in complex with murine Abeta-pE3-18PEGb. Determined by X-ray diffraction at 1.6 Å resolution. Released 28 Jun 2017.

Method: X-ray diffraction
Resolution: 1.6 Å
Organism: Mus musculus
Chains: 3
Atoms: 3,785
Mol. weight: 50.6 kDa
Released: 28 Jun 2017

Explore 5MYK in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5MYK contains 17 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 A: 9 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	30	1	3
β-strand	36	1	3
β-strand	38-43	6	2
β-strand	50-54	5	2
β-strand	58-59	2	2
α-helix	60	1
β-strand	67-72	6	1
β-strand	75-80	6	1
α-helix	85-87	3
β-strand	89-95	7	2
α-helix	101	1
β-strand	102-103	2	2
β-strand	107-111	5	2
β-strand	116	1	4
α-helix	117-118	2
β-strand	119-123	5	5
α-helix	124-126	3
α-helix	127-131	5
β-strand	134-144	11	5
β-strand	145	1	4
β-strand	150-155	6	6
β-strand	158-160	3	6
β-strand	164-168	5	5
α-helix	169-172	4
β-strand	178-187	10	5
α-helix	188-192	5
β-strand	196-203	8	6
β-strand	206-215	10	6
α-helix	216-218	3

Chain B: 7 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	7
β-strand	10-12	3	8
β-strand	18-25	8	7
α-helix	29-31	3
β-strand	34-39	6	8
β-strand	46-51	6	8
β-strand	58-60	3	8
β-strand	68-73	6	7
α-helix	74-76	3
β-strand	78-83	6	7
α-helix	88-90	3
β-strand	92-101	10	8
β-strand	105-112	8	8
β-strand	116-120	5	8
α-helix	123-125	3
β-strand	126	1	9
α-helix	127-128	2
β-strand	129-133	5	10
β-strand	144-154	11	10
β-strand	155	1	9
β-strand	160-163	4	11
α-helix	164-166	3
β-strand	168	1	11
β-strand	173-180	8	10
β-strand	183-193	11	10
β-strand	203-208	6	11
α-helix	209-211	3
β-strand	213-218	6	11

Chain C: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
β-strand	2-3	2	8
α-helix	4-5	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Fab c#17 light chain	A	protein	219	Mus musculus
Fab c#17 heavy chain	B	protein	231	Mus musculus
Amyloid beta A4 protein	C	protein	16	Mus musculus	P12023 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5MYK_1 Fab c#17 light chain (chains A)
DVVMTQTPLSLPVSLGDQASISCRSSQSLVHSDGNTYLHWYLQKPGQSPKLLIYKVSNRF
SGVPDRFSGSGSGTDFTLKISRVEAEDLGVYFCSQSTHVPPTFGGGTKLEIKRADAAPTV
SIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSM
SSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Sequence of entity 2 (B), FASTA

>5MYK_2 Fab c#17 heavy chain (chains B)
EVKLVESGGGLVQPGGSRKLSCAASGFTFSDYGMAWVRQAPGKGPEWVAFISNLAYSIYY
ADTVTGRFTISRENAKNTLYLEMSSLRSEDTAMYYCARYDYDNILDYVMDYWGQGTSVTV
SSAKTTPPSVYPLAPGCGDTTGSSVTLGCLVKGYFPESVTVTWNSGSLSSSVHTFPALLQ
SGLYTMSSSVTVPSSTWPSQTVTCSVAHPASSTTVDKKLEPSGPISTINPC

Sequence of entity 3 (C), FASTA

>5MYK_3 Amyloid beta A4 protein (chains C)
QFGHDSGFEVRHQKLV

Primary citation

Structural and functional analyses of pyroglutamate-amyloid-beta-specific antibodies as a basis for Alzheimer immunotherapy. Piechotta, A., Parthier, C., Kleinschmidt, M. et al. J Biol Chem (2017) 292:12713-12724. DOI 10.1074/jbc.M117.777839 · PubMed

Other PDB entries of the same protein (UniProt P12023 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4YN0 2.2 Å, Crystal structure of APP E2 domain in complex with DR6 CRD domain
8S4Y 2.7 Å, Crystal structure of an APP-talin (F2F3) chimera
7MRN 3.5 Å, Mouse CNTN5 APP complex
8BG9 3.5 Å, Murine amyloid-beta filaments with the Arctic mutation (E22G) from APP(NL-G-F) mouse…
2ROZ Structure of the C-terminal PID Domain of Fe65L1 Complexed with the Cytoplasmic Tail of…

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