5U5M

CRYSTAL STRUCTURE OF I83E MEDITOPE-ENABLED TRASTUZUMAB WITH AZIDO-MEDITOPE

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
IMGT Antibody Annotation
SAbDab Antibody Annotation
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Protein Modification Annotation

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C [auth E]	SCOP2B Superfamily	Immunoglobulin-binding domains-like	8085561	3000399	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B	V-set_8	e5u5mB1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_8	ECOD (1.6)
B	C1-set_1	e5u5mB2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_1	ECOD (1.6)
C [auth E]	B1	e5u5mE1	A: a+b two layers	X: beta-Grasp	H: Immunoglobulin-binding domains (From Topology)	T: Immunoglobulin-binding domains	F: B1	ECOD (1.6)
D [auth C]	B	e5u5mC1	A: alpha bundles	X: immunoglobulin/albumin-binding domain-like	H: Bacterial immunoglobulin/albumin-binding domains (From Topology)	T: Bacterial immunoglobulin/albumin-binding domains	F: B	ECOD (1.6)
A	C1-set_4	e5u5mA2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_4	ECOD (1.6)
A	V-set	e5u5mA1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
C [auth E]	3.10.20.10	Alpha Beta	Roll	Ubiquitin-like (UB roll)		CATH (4.3.0)
D [auth C]	1.20.5.420	Mainly Alpha	Up-down Bundle	Single alpha-helices involved in coiled-coils or other helix-helix interfaces	Immunoglobulin FC, subunit C	CATH (4.3.0)
A	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)

IMGT Antibody Annotation IMGT Database Homepage

Chain	Protein Name	Description	Organism Name	Gene Allele Name(s)	Domain Name(s)	Receptor Type	Receptor Description	Provenance Source
B	Fab Memab trastuzumab	VH-CH1	Homo sapiens (human)	IGHV3-6601, IGHV3-6602, IGHV3-6604, IGHJ401, IGHJ402, IGHJ403, IGHG101, IGHG102, IGHG104, IGHG105, IGHG112, IGHG114, IGHG113, IGHG109, IGHG110, IGHG107, IGHG1*11	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_KAPPA	IMGT (202445-0)
A	Fab Memab trastuzumab	L-KAPPA	Homo sapiens (human)	IGKV1-3901, IGKV1D-3901, IGKJ101, IGKJ401, IGKJ402, IGKC01	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-1_KAPPA	IMGT (202445-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
B	Heavy Chain	IGHV3	-	immunoglobulin g binding protein a \| protein l	SAbDab (2024-11-15)
A	Light Chain	IGKV1	Kappa	immunoglobulin g binding protein a \| protein l	SAbDab (2024-11-15)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C [auth E]	PF02246	Protein L b1 domain (B1)	Protein L b1 domain	Protein L is a bacterial protein with immunoglobulin (Ig) light chain-binding properties. It contains a number of homologous b1 repeats towards the N-terminus. These repeats have been found to be responsible for the interaction of protein L with Ig ...	Protein L is a bacterial protein with immunoglobulin (Ig) light chain-binding properties. It contains a number of homologous b1 repeats towards the N-terminus. These repeats have been found to be responsible for the interaction of protein L with Ig light chains [1].	Domain
D [auth C]	PF02216	B domain (B)	B domain	This family contains the B domain of Staphylococcal protein A, which specifically binds to the Fc portion of immunoglobulin G.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B	MEMAB TRASTUZUMAB, HEAVY CHAIN	-	-	-
C [auth E]	Protein L	protein-containing complex binding binding immunoglobulin binding IgG binding	-	-
D [auth C]	Immunoglobulin G binding protein A	protein-containing complex binding binding immunoglobulin binding IgG binding	-	cellular anatomical structure extracellular region
E [auth D]	AZIDO-PEG4-MEDITOPE	-	-	-
A	MEMAB TRASTUZUMAB, LIGHT CHAIN	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C [auth E]	IPR009063	Immunoglobulin/albumin-binding domain superfamily	Homologous Superfamily
C [auth E]	IPR020840	Extracellular matrix-binding protein ebh, GA module	Domain
C [auth E]	IPR003147	Protein L, Ig light chain-binding	Repeat
C [auth E]	IPR040912	Repeat of unknown function DUF5633	Repeat
C [auth E]	IPR002988	Protein G-related albumin-binding (GA) module	Domain
C [auth E]	IPR035152	GA-like domain	Domain
C [auth E]	IPR019931	LPXTG cell wall anchor domain	Domain
D [auth C]	IPR009063	Immunoglobulin/albumin-binding domain superfamily	Homologous Superfamily
D [auth C]	IPR005877	YSIRK Gram-positive signal peptide	Domain
D [auth C]	IPR036779	LysM domain superfamily	Homologous Superfamily
D [auth C]	IPR005038	Octapeptide repeat	Repeat
D [auth C]	IPR003132	Protein A, Ig-binding domain	Domain
D [auth C]	IPR018392	LysM domain	Domain
D [auth C]	IPR019931	LPXTG cell wall anchor domain	Domain

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
E [auth D]	2GX	Parent Component: PHE
E [auth D]	56C
E [auth D]	ACE	RESID: AA0041 , AA0042 , AA0043 , AA0044 , AA0045 , AA0046 , AA0049 , AA0050 , AA0051 , AA0052 , AA0053 , AA0054 , AA0354 PSI-MOD : N-acetyl-L-alanine MOD:00050 , N-acetyl-L-aspartic acid MOD:00051 , N-acetyl-L-cysteine MOD:00052 , N-acetyl-S-archeol-cysteine MOD:00897 , N-acetyl-L-glutamic acid MOD:00053 , N-acetyl-L-glutamine MOD:00054 , N-acetylglycine MOD:00055 , N-acetyl-L-methionine MOD:00058 , N-acetyl-L-proline MOD:00059 , N-acetyl-L-serine MOD:00060 , N,O-diacetylated L-serine MOD:00648 , N-acetyl-L-threonine MOD:00061 , N-acetyl-L-tyrosine MOD:00062 , N-acetyl-L-valine MOD:00063 , N2-acetyl-L-arginine MOD:00359

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.