5U3D: Meditope enabled trastuzumab I83E variant

Structure of meditope enabled trastuzumab I83E variant. Determined by X-ray diffraction at 1.77 Å resolution. Released 14 Mar 2018.

Method: X-ray diffraction
Resolution: 1.77 Å
Organisms: Homo sapiens, Finegoldia magna, Staphylococcus aureus
Chains: 4
Atoms: 5,161
Mol. weight: 60.45 kDa
Ligands: MRY
Released: 14 Mar 2018

Explore 5U3D in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5U3D contains 25 α-helices and 53 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: 9 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	1
β-strand	10-14	5	2
β-strand	19-25	7	1
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	102-107	6	2
β-strand	111	1	3
α-helix	112-113	2
β-strand	114-118	5	4
α-helix	119-121	3
α-helix	122-125	4
β-strand	129-139	11	4
β-strand	140	1	3
β-strand	145-150	6	5
β-strand	153-154	2	5
α-helix	155	1
β-strand	159-163	5	4
α-helix	164-167	4
β-strand	173-182	10	4
α-helix	183-188	6
β-strand	191-197	7	5
β-strand	205-210	6	5

Chain B: 10 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	6
β-strand	11-12	2	7
β-strand	18-25	8	6
α-helix	29-31	3
β-strand	33-39	7	8
β-strand	45-52	8	8
β-strand	57-60	4	8
β-strand	65	1	6
β-strand	68-73	6	6
α-helix	74-76	3
β-strand	78-83	6	6
α-helix	88-90	3
β-strand	92-99	8	8
α-helix	101-103	3
β-strand	110	1	8
β-strand	114-116	3	8
β-strand	117-118	2	7
α-helix	122-123	2
β-strand	124	1	9
α-helix	125-126	2
β-strand	127-131	5	10
β-strand	138-139	2	10
β-strand	142-152	11	10
β-strand	153	1	9
β-strand	158-161	4	11
α-helix	162-164	3
β-strand	166	1	11
β-strand	170-172	3	10
α-helix	173-175	3
β-strand	176-177	2	10
β-strand	183-192	10	10
α-helix	193-195	3
β-strand	196	1	12
β-strand	199	1	12
β-strand	202-207	6	11
α-helix	208-210	3
β-strand	212-217	6	11

Chain C: 4 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	3	1	12
α-helix	5-16	12
α-helix	22-34	13
α-helix	36-38	3
α-helix	39-52	14

Chain E: 2 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	21-28	8	2
β-strand	34-41	8	2
α-helix	43-61	19
β-strand	64-69	6	2
α-helix	70-72	3
β-strand	74-79	6	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Memab trastuzumab FAB light chain I83E	A	protein	214	Homo sapiens
Memab trastuzumab FAB heavy chain	B	protein	223	Homo sapiens
Protein L	E	protein	65	Finegoldia magna	Q51918 (AlphaFold model)
Immunoglobulin G binding protein A	C	protein	54	Staphylococcus aureus	P02976 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5U3D_1 MEMAB TRASTUZUMAB FAB LIGHT CHAIN I83E (chains A)
DIQMTQSPILLSASVGDRVTITCRASQDVNTAVAWYQQRTNGSPRLLIYSASFLYSGVPS
RFSGSRSGTDFTLTISSLQPEDEADYYCQQHYTTPPTFGAGTKVEIKRTVAAPSVFIFPP
SDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT
LSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 2 (B), FASTA

>5U3D_2 MEMAB TRASTUZUMAB FAB HEAVY CHAIN (chains B)
EVQLVESGGGLVQPGGSLRLSCAASGFNIKDTYIHWVRQSPGKGLEWVARIYPTNGYTRY
ADSVKGRFTISADTSKNTAYLQMNSLRAEDTAIYYCSRWGGDGFYAMDYWGQGTLVTVSS
ASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSS
GLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC

Sequence of entity 3 (E), FASTA

>5U3D_3 Protein L (chains E)
SGSEVTIKVNLIFADGKIQTAEFKGTFEEATAEAYRYAALLAKVNGEYTADLEDGGNHMN
IKFAG

Sequence of entity 4 (C), FASTA

>5U3D_4 Immunoglobulin G binding protein A (chains C)
GSYNKDQQSAFYEILNMPNLNEAQRNGFIQSLKDDPSQSTNVLGEAKKLNESQA

Ligands and cofactors

ID	Name	Formula	Copies
MRY	Meso-erythritol	C4 H10 O4	1

Primary citation

Meditope Enabled Trastuzumab I83E Variant. Bzymek, K.P., Avery, K.N., Zer, C. et al. To be published.

Other PDB entries of the same protein (UniProt Q51918 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5U6A 1.74 Å, Crystal structure of I83E meditope-enabled trastuzumab with azido-PEG3-meditope
5U5F 1.81 Å, Meditope enabled trastuzumab I83E variant in complex with (ac) CQFDA(PH)2STRRLRCGGSK
6B9Z 1.82 Å, Trastuzumab Fab v3
5U5M 1.88 Å, Crystal structure of I83E meditope-enabled trastuzumab with azido-meditope
6BAH 1.9 Å, Trastuzumab Fab v3 with 5-diphenyl meditope variant
4IOI 1.95 Å, Meditope-enabled trastuzumab in complex with CQFDLSTRRLKC
4HJG 2.0 Å, Meditope-enabled trastuzumab
4HKZ 2.08 Å, Trastuzumab Fab complexed with Protein L and Protein A fragments
6B9Y 2.14 Å, Trastuzumab Fab v3 in complex with 5-phenyl meditope variant
6BAE 2.14 Å, Trastuzumab Fab v3 in complex with CQFDLSTRRLKC
1YMH 2.6 Å, anti-HCV Fab 19D9D6 complexed with protein L (PpL) mutant A66W
1HEZ 2.7 Å, Structure of P. magnus protein L bound to a human IgM Fab.

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