4IOI - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Title :   MEDITOPE-ENABLED TRASTUZUMAB IN COMPLEX WITH CQFDLSTRRLKC

Authors :   K. P. Bzymek, C. Zer, K. N. Avery, J. C. Williams

Date :   07 Jan 13 (Deposition) - 09 Oct 13 (Release) - 06 Nov 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.95

Chains :   Asym./Biol. Unit : A,B,C,E,H

Keywords :   Monoclonal Antibody, Immune System, Cancer Immunotherapy (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. M. Donaldson, C. Zer, K. N. Avery, K. P. Bzymek, D. A. Horne, J. C. Williams
Identification And Grafting Of A Unique Peptide-Binding Sit In The Fab Framework Of Monoclonal Antibodies.
Proc. Natl. Acad. Sci. Usa V. 110 17456 2013
PubMed-ID: 24101516 | Reference-DOI: 10.1073/PNAS.1307309110

Molecule 1 - TRASTUZUMAB LIGHT CHAIN
	Chains	:	A
	Engineered	:	YES
	Expression System	:	MUS MUSCULUS
	Expression System Taxid	:	10090
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

Molecule 2 - TRASTUZUMAB HEAVY CHAIN
	Chains	:	B
	Engineered	:	YES
	Expression System	:	MUS MUSCULUS
	Expression System Taxid	:	10090
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

Molecule 3 - IMMUNOGLOBULIN G-BINDING PROTEIN A
	Chains	:	H
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	SPA, SAV0111
	Organism Scientific	:	STAPHYLOCOCCUS AUREUS
	Organism Taxid	:	158878
	Strain	:	MU50 / ATCC 700699
	Synonym	:	IGG-BINDING PROTEIN A, STAPHYLOCOCCAL PROTEIN A

Molecule 4 - PROTEIN L
	Chains	:	E
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Mutation	:	YES
	Organism Scientific	:	FINEGOLDIA MAGNA
	Organism Taxid	:	1260

Molecule 5 - MEDITOPE
	Chains	:	C
	Engineered	:	YES
	Synthetic	:	YES

		1	2	3	4	5
Asymmetric/Biological Unit	:	A	B	C	E	H

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 4IOI)

(no "Site" information available for 4IOI)

Asymmetric/Biological Unit

No.	Residues
1	A:23	-	A:88
2	A:134	-	A:194
3	B:22	-	B:96
4	B:147	-	B:203
5	C:1	-	C:12

Asymmetric/Biological Unit

No.	Residues
1	Ser A:7	-	Pro A:8
2	Thr A:94	-	Pro A:95
3	Tyr A:140	-	Pro A:141
4	Phe B:153	-	Pro B:154
5	Glu B:155	-	Pro B:156

(no "SAP(SNP)/Variant" information available for 4IOI)

(no "PROSITE Motif" information available for 4IOI)

(no "Exon" information available for 4IOI)

Asymmetric/Biological Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
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Chain A from PDB  Type:PROTEIN  Length:214
                                                                                                                                                                                                                                                      
               SCOP domains d4ioia1 A:1-107 automated matches                                                                          d4ioia2 A:108-214 automated matches                                                                         SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeeee......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhhhh.eeeeeee.......eeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ioi A   1 DIQMTQSPILLSASVGDRVTITCRASQDVNTAVAWYQQRTNGSPRLLIYSASFLYSGVPSRFSGSRSGTDFTLTISSLQPEDIADYYCQQHYTTPPTFGAGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC 214
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210

Chain B from PDB  Type:PROTEIN  Length:220
                                                                                                                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee..hhhhheeeeeeee...eeeeeeee......eee.......eeeeeehhh.eeeeee...hhhhheeeeeeee.hhhh..eeee...eeeee........eeeee......ee..eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhh.....eeeeeehhhheeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ioi B   1 EVQLVESGGGLVQPGGSLRLSCAASGFNIKDTYIHWVRQSPGKGLEWVARIYPTNGYTRYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAIYYCSRWGGDGFYAMDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEP 220
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220

Chain C from PDB  Type:PROTEIN  Length:12
                                            
               SCOP domains ------------ SCOP domains
               CATH domains ------------ CATH domains
               Pfam domains ------------ Pfam domains
         Sec.struct. author .eee....eee. Sec.struct. author
                 SAPs(SNPs) ------------ SAPs(SNPs)
                    PROSITE ------------ PROSITE
                 Transcript ------------ Transcript
                 4ioi C   1 CQFDLSTRRLKC  12
                                    10

Chain E from PDB  Type:PROTEIN  Length:63
                                                                                               
               SCOP domains d4ioie_ E: automated matches                                    SCOP domains
               CATH domains --------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeee.....eeeeeeeehhhhhhhhhhhhhhhhhhhhh.eeeeee....eeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------- Transcript
                 4ioi E  19 SEVTIKVNLIFADGKIQTAEFKGTFEEATAEAYRYAALLAKVNGEYTADLEDGGNHMNIKFAG  81
                                    28        38        48        58        68        78

Chain H from PDB  Type:PROTEIN  Length:53
                                                                                     
               SCOP domains d4ioih_ H: automated matches                          SCOP domains
               CATH domains ----------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhh...hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------- Transcript
                 4ioi H   2 SYNKDQQSAFYEILNMPNLNEAQRNGFIQSLKDDPSQSTNVLGEAKKLNESQA  54
                                    11        21        31        41        51

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
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	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

(no "CATH Domain" information available for 4IOI)

(no "Pfam Domain" information available for 4IOI)

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	Ligands, Modified Residues, Ions
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(no "Sites" information available for 4ioi)

	Cis Peptide Bonds
		Glu B:155 - Pro B:156	[ RasMol ]
		Phe B:153 - Pro B:154	[ RasMol ]
		Ser A:7 - Pro A:8	[ RasMol ]
		Thr A:94 - Pro A:95	[ RasMol ]
		Tyr A:140 - Pro A:141	[ RasMol ]

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UniProtKB/Swiss-Prot
	SPA_STAAM \| P0A015	:	4hjg 4hkz
UniProtKB/TrEMBL
	Q51918_FINMA \| Q51918	:	1hez 1ymh 1ynt 2fs1 4hjg 4hkz

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (5, 5)

Cis Peptide Bonds (5, 5)

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SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

Sequences/Alignments

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SCOP Domains (4, 4)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (6, 8)

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