4ZFO - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   J22.9-XI: CHIMERIC MOUSE/HUMAN ANTIBODY AGAINST HUMAN BCMA (CD269)

Authors :   S. F. Marino, O. Daumke, D. Olal

Date :   21 Apr 15 (Deposition) - 20 May 15 (Release) - 12 Aug 15 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

Chains :   Asym. Unit : A,B,F,H,K,L
Biol. Unit 1: A,B,F  (1x)
Biol. Unit 2: H,K,L  (1x)

Keywords :   Antibody Fab-Ligand Complex Anti-Bcma Anti-Tumor, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   F. Oden, S. F. Marino, J. Brand, S. Scheu, C. Kriegel, D. Olal, A. Takvorian, J. Westermann, B. Yilmaz, M. Hinz, O. Daumke, U. E. Hopken, G. Muller, M. Lipp
Potent Anti-Tumor Response By Targeting B Cell Maturation Antigen (Bcma) In A Mouse Model Of Multiple Myeloma.
Mol Oncol V. 9 1348 2015
PubMed-ID: 25953704 | Reference-DOI: 10.1016/J.MOLONC.2015.03.010

Molecule 1 - TUMOR NECROSIS FACTOR RECEPTOR SUPERFAMILY MEMBER 17
	Chains	:	F, K
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGEX6P-1
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Variant	:	ROSETTA2
	Expression System Vector Type	:	PLASMID
	Fragment	:	EXTRACELLULAR (N-TERMINAL) DOMAIN, UNP RESIDUES 1-54
	Gene	:	TNFRSF17, BCM, BCMA
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	B-CELL MATURATION PROTEIN, BCMA, CD269

Molecule 2 - J22.9-XI FAB, LIGHT CHAIN
	Chains	:	L
	Engineered	:	YES
	Expression System	:	HOMO SAPIENS
	Expression System Cell Line	:	HEK293_6E
	Expression System Plasmid	:	PTT5
	Expression System Taxid	:	9606
	Expression System Vector Type	:	PLASMID
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Other Details	:	FAB LIGHT CHAIN FRAGMENT OF ANTI-BCMA ANTIBODY J22.9- XI

Molecule 3 - J22.9-XI FAB, HEAVY CHAIN
	Chains	:	H, A
	Engineered	:	YES
	Expression System	:	HOMO SAPIENS
	Expression System Cell Line	:	HEK293_6E
	Expression System Plasmid	:	PTT5
	Expression System Taxid	:	9606
	Expression System Vector Type	:	PLASMID
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Other Details	:	FAB HEAVY CHAIN FRAGMENT OF ANTI-BCMA ANTIBODY J22.9- XI

Molecule 4 - J22.9-XI FAB, LIGHT CHAIN
	Chains	:	B
	Engineered	:	YES
	Expression System	:	HOMO SAPIENS
	Expression System Cell Line	:	HEK293_6E
	Expression System Plasmid	:	PTT5
	Expression System Taxid	:	9606
	Expression System Vector Type	:	PLASMID
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Other Details	:	FAB LIGHT CHAIN FRAGMENT OF ANTI-BCMA ANTIBODY J22.9- XI

		1	2	3	4	5	6
Asymmetric Unit	:	A	B	F	H	K	L
Biological Unit 1 (1x)	:	A	B	F
Biological Unit 2 (1x)	:				H	K	L

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 5)

No.	Name	Count	Type	Full Name
1	BTB	2	Ligand/Ion	2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
2	CU	3	Ligand/Ion	COPPER (II) ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	BTB	1	Ligand/Ion	2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
2	CU	-1	Ligand/Ion	COPPER (II) ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	BTB	1	Ligand/Ion	2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
2	CU	-1	Ligand/Ion	COPPER (II) ION

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP B:1 , HOH B:553 , ASP L:1 , HOH L:563	binding site for residue CU L 301
2	AC2	SOFTWARE	HIS L:189 , BTB L:303	binding site for residue CU L 302
3	AC3	SOFTWARE	TYR A:103 , ASP L:185 , HIS L:189 , CU L:302 , HOH L:461	binding site for residue BTB L 303
4	AC4	SOFTWARE	HIS B:189 , BTB B:302	binding site for residue CU B 301
5	AC5	SOFTWARE	LYS A:213 , VAL A:214 , ASP A:215 , ASP B:185 , LYS B:188 , HIS B:189 , CU B:301 , HOH B:401	binding site for residue BTB B 302

Asymmetric Unit

No.	Residues
1	A:22	-	A:96
2	A:147	-	A:203
3	B:23	-	B:88
4	B:134	-	B:194
5	F:8	-	F:21
6	F:24	-	F:37
7	F:28	-	F:41
8	H:22	-	H:96
9	H:147	-	H:203
10	K:8	-	K:21
11	K:24	-	K:37
12	K:28	-	K:41
13	L:23	-	L:88
14	L:134	-	L:194

Asymmetric Unit

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

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

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

(no "Exon" information available for 4ZFO)

Asymmetric 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
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:215
                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..eee.....eeeeeeee..hhhhh.eeeeee.....eeeeeee......eee.hhhh..eeeeeehhh.eeeeee...hhhhheeeeeeeeeee..eeeeee...eeeee........eeeee.....eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhh.....eeeeeehhhheeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4zfo A   1 QVQLQQSGGGLVQPGGSLKLSCAASGIDFSRYWMSWVRRAPGKGLEWIGEINPDSSTINYAPSLKDKFIISRDNAKNTLYLQMSKVRSEDTALYYCASLYYDYGDAMDYWGQGTSVTVSSASTKGPSVFPLAPSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEP 220
                                    10        20        30        40        50        60        70        80        90       100       110       120       130  ||   145       155       165       175       185       195       205       215     
                                                                                                                                                              133|                                                                                 
                                                                                                                                                               139

Chain B from PDB  Type:PROTEIN  Length:213
                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee....eeee.....eeeeeee.......eeeeee......eeeee...ee.......eeeee...eeeeee...hhhhh.eeeeee......ee...eeeee.......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhh...eeeeeee.......eeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4zfo B   1 DIVMTQSQRFMTTSVGDRVSVTCKASQSVDSNVAWYQQKPRQSPKALIFSASLRFSGVPARFTGSGSGTDFTLTISNLQSEDLAEYFCQQYNNYPLTFGAGTKLELKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGE 213
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210

Chain F from PDB  Type:PROTEIN  Length:36
                                                                    
               SCOP domains ------------------------------------ SCOP domains
               CATH domains ------------------------------------ CATH domains
               Pfam domains ------------------------------------ Pfam domains
         Sec.struct. author ......eeee....eeee.hhhh.....hhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------ PROSITE
                 Transcript ------------------------------------ Transcript
                 4zfo F   6 GQCSQNEYFDSLLHACIPCQLRCSSNTPPLTCQRYC  41
                                    15        25        35

Chain H from PDB  Type:PROTEIN  Length:216
                                                                                                                                                                                                                                                        
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeee..eee.....eeeeeeee........eeeeee.....eeeeeee......eee.......eeeeeehhh.eeeeee...hhhhheeeeeeeeeee..eeeeee...eeeee........eeeee.....eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhh.....eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4zfo H   1 QVQLQQSGGGLVQPGGSLKLSCAASGIDFSRYWMSWVRRAPGKGLEWIGEINPDSSTINYAPSLKDKFIISRDNAKNTLYLQMSKVRSEDTALYYCASLYYDYGDAMDYWGQGTSVTVSSASTKGPSVFPLAPSSGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPA 221
                                    10        20        30        40        50        60        70        80        90       100       110       120       130    || 145       155       165       175       185       195       205       215      
                                                                                                                                                                135|                                                                                
                                                                                                                                                                 141

Chain K from PDB  Type:PROTEIN  Length:35
                                                                   
               SCOP domains ----------------------------------- SCOP domains
               CATH domains ----------------------------------- CATH domains
               Pfam domains ----------------------------------- Pfam domains
         Sec.struct. author .....eeee....eeee.hhhh.....hhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------- PROSITE
                 Transcript ----------------------------------- Transcript
                 4zfo K   7 QCSQNEYFDSLLHACIPCQLRCSSNTPPLTCQRYC  41
                                    16        26        36

Chain L from PDB  Type:PROTEIN  Length:214
                                                                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee....eeee.....eeeeeee.......eeeeee......eeeee...ee.......eeee....eeeeee...hhhhh.eeeeee......ee...eeeee.......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhh...eeeeeee.......eeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4zfo L   1 DIVMTQSQRFMTTSVGDRVSVTCKASQSVDSNVAWYQQKPRQSPKALIFSASLRFSGVPARFTGSGSGTDFTLTISNLQSEDLAEYFCQQYNNYPLTFGAGTKLELKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEA 214
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	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 "SCOP Domain" information available for 4ZFO)

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

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

Asymmetric Unit(hide GO term definitions)

Asymmetric Unit
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	Cis Peptide Bonds
		Glu A:155 - Pro A:156	[ RasMol ]
		Glu H:155 - Pro H:156	[ RasMol ]
		Phe A:153 - Pro A:154	[ RasMol ]
		Phe H:153 - Pro H:154	[ RasMol ]
		Tyr B:140 - Pro B:141	[ RasMol ]
		Tyr B:94 - Pro B:95	[ RasMol ]
		Tyr L:140 - Pro L:141	[ RasMol ]
		Tyr L:94 - Pro L:95	[ RasMol ]

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(no "Related Entries Specified in the PDB File" available for 4ZFO)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 5)

Sites (5, 5)

SS Bonds (14, 14)

Cis Peptide Bonds (8, 8)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

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Gene Ontology (12, 12)

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