4IOI: Meditope-enabled trastuzumab

Meditope-enabled trastuzumab in complex with CQFDLSTRRLKC. Determined by X-ray diffraction at 1.95 Å resolution. Released 9 Oct 2013.

Method: X-ray diffraction
Resolution: 1.95 Å
Organisms: Homo sapiens, Staphylococcus aureus, Finegoldia magna
Chains: 5
Atoms: 4,964
Mol. weight: 61.87 kDa
Released: 9 Oct 2013

Explore 4IOI in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4IOI contains 24 α-helices and 53 β-strands across 5 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, 26 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	33-40	8	2
β-strand	44-52	9	2
β-strand	57-60	4	2
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	2
α-helix	101-103	3
β-strand	107-110	4	2
β-strand	114-116	3	2
β-strand	117-118	2	7
α-helix	122-123	2
β-strand	124	1	8
α-helix	125-126	2
β-strand	127-131	5	9
β-strand	138-139	2	9
β-strand	142-152	11	9
β-strand	153	1	8
β-strand	158-161	4	10
α-helix	162-164	3
β-strand	166	1	10
β-strand	170-172	3	9
α-helix	173-175	3
β-strand	176-177	2	9
β-strand	183-192	10	9
α-helix	193-195	3
β-strand	196	1	11
β-strand	199	1	11
β-strand	202-207	6	10
α-helix	208-210	3
β-strand	212-217	6	10

Chain C: 0 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	2-4	3	12
β-strand	9-11	3	12

Chain E: 1 helix, 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
β-strand	74-79	6	2

Chain H: 4 helices, 0 β-strands

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

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Trastuzumab light chain	A	protein	214	Homo sapiens
Trastuzumab heavy chain	B	protein	223	Homo sapiens
Immunoglobulin G-binding protein A	H	protein	55	Staphylococcus aureus	P0A015 (AlphaFold model)
Protein L	E	protein	65	Finegoldia magna	Q51918 (AlphaFold model)
meditope	C	protein	12

Sequence of entity 1 (A), FASTA

>4IOI_1 Trastuzumab light chain (chains A)
DIQMTQSPILLSASVGDRVTITCRASQDVNTAVAWYQQRTNGSPRLLIYSASFLYSGVPS
RFSGSRSGTDFTLTISSLQPEDIADYYCQQHYTTPPTFGAGTKVEIKRTVAAPSVFIFPP
SDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT
LSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 2 (B), FASTA

>4IOI_2 Trastuzumab heavy chain (chains B)
EVQLVESGGGLVQPGGSLRLSCAASGFNIKDTYIHWVRQSPGKGLEWVARIYPTNGYTRY
ADSVKGRFTISADTSKNTAYLQMNSLRAEDTAIYYCSRWGGDGFYAMDYWGQGTLVTVSS
ASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSS
GLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC

Sequence of entity 3 (H), FASTA

>4IOI_3 Immunoglobulin G-binding protein A (chains H)
SGSYNKDQQSAFYEILNMPNLNEAQRNGFIQSLKDDPSQSTNVLGEAKKLNESQA

Sequence of entity 4 (E), FASTA

>4IOI_4 Protein L (chains E)
SGSEVTIKVNLIFADGKIQTAEFKGTFEEATAEAYRYAALLAKVNGEYTADLEDGGNHMN
IKFAG

Sequence of entity 5 (C), FASTA

>4IOI_5 meditope (chains C)
CQFDLSTRRLKC

Primary citation

Identification and grafting of a unique peptide-binding site in the Fab framework of monoclonal antibodies. Donaldson, J.M., Zer, C., Avery, K.N. et al. Proc Natl Acad Sci U S A (2013) 110:17456-17461. DOI 10.1073/pnas.1307309110 · PubMed

Other PDB entries of the same protein (UniProt P0A015 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4HJG 2.0 Å, Meditope-enabled trastuzumab
4HKZ 2.08 Å, Trastuzumab Fab complexed with Protein L and Protein A fragments
8JXS 3.0 Å, Structure of nanobody-bound DRD1_PF-6142 complex
8JXR 3.57 Å, Structure of nanobody-bound DRD1_LSD complex

Browse structure collections

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