43CA - 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)

Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Title :   CRYSTALLOGRAPHIC STRUCTURE OF THE ESTEROLYTIC AND AMIDOLYTIC 43C9 ANTIBODY WITH BOUND P-NITROPHENOL

Authors :   M. M. Thayer, E. D. Getzoff, V. A. Roberts

Date :   10 Mar 99 (Deposition) - 18 Aug 99 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

Chains :   Asym. Unit : A,B,C,D,E,F,G,H
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: C,D  (1x)
Biol. Unit 3: E,F  (1x)
Biol. Unit 4: G,H  (1x)

Keywords :   Immunoglobulin, Catalytic Antibody (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. M. Thayer, E. H. Olender, A. S. Arvai, C. K. Koike, I. L. Canestrelli, J. D. Stewart, S. J. Benkovic, E. D. Getzoff, V. A. Roberts
Structural Basis For Amide Hydrolysis Catalyzed By The 43C9 Antibody.
J. Mol. Biol. V. 291 329 1999
PubMed-ID: 10438624 | Reference-DOI: 10.1006/JMBI.1999.2960
(for further references see the PDB file header)

Molecule 1 - PROTEIN (IMMUNOGLOBULIN (LIGHT CHAIN))
	Chains	:	A, C, E, G
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Cell Line	:	BL21(DE3)
	Expression System Taxid	:	562
	Fragment	:	FV
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090

Molecule 2 - PROTEIN (IMMUNOGLOBULIN (HEAVY CHAIN))
	Chains	:	B, D, F, H
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Cell Line	:	BL21(DE3)
	Expression System Taxid	:	562
	Fragment	:	FV
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090

		1	2	3	4	5	6	7	8
Asymmetric Unit	:	A	B	C	D	E	F	G	H
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			C	D
Biological Unit 3 (1x)	:					E	F
Biological Unit 4 (1x)	:							G	H

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 4)

No.	Name	Count	Type	Full Name
1	NPO	4	Ligand/Ion	P-NITROPHENOL

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	NPO	1	Ligand/Ion	P-NITROPHENOL

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	NPO	1	Ligand/Ion	P-NITROPHENOL

Biological Unit 3 (1, 1)

No.	Name	Count	Type	Full Name
1	NPO	1	Ligand/Ion	P-NITROPHENOL

Biological Unit 4 (1, 1)

No.	Name	Count	Type	Full Name
1	NPO	1	Ligand/Ion	P-NITROPHENOL

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	AUTHOR	HIS A:91 , ARG A:96	CATALYTIC SITE IS BELIEVED TO INCLUDE: HIS 91 IN THE VARIABLE LIGHT CHAIN - NUCLEOPHILE THAT FORMS A COVALENT BOND TO THE SUBSTRATE ARG 96 IN THE VARIABLE LIGHT CHAIN - SIDE CHAIN STABILIZES NEGATIVE CHARGE FORMED IN THE TRANSITION STATES OF THE REACTION
2	AC2	AUTHOR	HIS C:91 , ARG C:96	CATALYTIC SITE IS BELIEVED TO INCLUDE: HIS 91 IN THE VARIABLE LIGHT CHAIN - NUCLEOPHILE THAT FORMS A COVALENT BOND TO THE SUBSTRATE ARG 96 IN THE VARIABLE LIGHT CHAIN - SIDE CHAIN STABILIZES NEGATIVE CHARGE FORMED IN THE TRANSITION STATES OF THE REACTION
3	AC3	AUTHOR	HIS E:91 , ARG E:96	CATALYTIC SITE IS BELIEVED TO INCLUDE: HIS 91 IN THE VARIABLE LIGHT CHAIN - NUCLEOPHILE THAT FORMS A COVALENT BOND TO THE SUBSTRATE ARG 96 IN THE VARIABLE LIGHT CHAIN - SIDE CHAIN STABILIZES NEGATIVE CHARGE FORMED IN THE TRANSITION STATES OF THE REACTION
4	AC4	AUTHOR	HIS G:91 , ARG G:96	CATALYTIC SITE IS BELIEVED TO INCLUDE: HIS 91 IN THE VARIABLE LIGHT CHAIN - NUCLEOPHILE THAT FORMS A COVALENT BOND TO THE SUBSTRATE ARG 96 IN THE VARIABLE LIGHT CHAIN - SIDE CHAIN STABILIZES NEGATIVE CHARGE FORMED IN THE TRANSITION STATES OF THE REACTION
5	AC5	SOFTWARE	ASN A:31 , TYR A:32 , LEU A:33 , ALA A:34 , TYR A:49 , PHE A:50 , HIS A:91 , TYR B:95 , PHE B:100B , HOH B:132	BINDING SITE FOR RESIDUE NPO A 921
6	AC6	SOFTWARE	ASN C:31 , TYR C:32 , LEU C:33 , ALA C:34 , TYR C:49 , PHE C:50 , HIS C:91 , PHE D:100B , HOH D:135	BINDING SITE FOR RESIDUE NPO C 922
7	AC7	SOFTWARE	TYR E:32 , LEU E:33 , ALA E:34 , TYR E:49 , PHE E:50 , HOH E:924 , TYR F:95 , PHE F:100B	BINDING SITE FOR RESIDUE NPO E 923
8	AC8	SOFTWARE	TYR G:32 , LEU G:33 , ALA G:34 , TYR G:49 , PHE G:50 , HIS G:91 , HOH G:588 , TYR H:95	BINDING SITE FOR RESIDUE NPO G 924

Asymmetric Unit

No.	Residues
1	A:23	-	A:88
2	B:22	-	B:92
3	C:23	-	C:88
4	D:22	-	D:92
5	E:23	-	E:88
6	F:22	-	F:92
7	G:23	-	G:88
8	H:22	-	H:92

Asymmetric Unit

No.	Residues
1	Thr A:7	-	Pro A:8
2	Ala A:94	-	Pro A:95
3	Thr C:7	-	Pro C:8
4	Ala C:94	-	Pro C:95
5	Thr E:7	-	Pro E:8
6	Ala E:94	-	Pro E:95
7	Thr G:7	-	Pro G:8
8	Ala G:94	-	Pro G:95

(no "SAP(SNP)/Variant" information available for 43CA)

(no "PROSITE Motif" information available for 43CA)

(no "Exon" information available for 43CA)

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:113
                                                                                                                                                  
               SCOP domains d43caa_ A: Immunoglobulin light chain kappa variable domain, VL-kappa                                             SCOP domains
               CATH domains 43caA00 A:1-107 Immunoglobulins                                                                                   CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee.............eeeeee......eeee.............eeeeee..eeeeee...hhhhheeeeeee...........eeeeee Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------- Transcript
                43ca A    1 DVVMTQTPSSLAMSVGQKVTMSCKSSQSLLNISNQKNYLAWYQQKPGQSPKLLVYFASTRESGVPDRFIGSGSGTDFTLTISSVQAEDQADYFCQQHYRAPRTFGGGTKLEIK  107
                                    10        20       27C|||     34        44        54        64        74        84        94       104   
                                                     27A|||||                                                                                
                                                      27B||||                                                                                
                                                       27C|||                                                                                
                                                        27D||                                                                                
                                                         27E|                                                                                
                                                          27F

Chain B from PDB  Type:PROTEIN  Length:117
 aligned with HVM44_MOUSE | P01820 from UniProtKB/Swiss-Prot  Length:115

    Alignment length:117
                                                                                                                         115                     
                                    29        39        49        59        69        79        89        99       109     |   -         -       
         HVM44_MOUSE     20 QVQLKESGPGLVAPSQSLSITCTVSGFSLTGYGVNWVRQPPGKGLEWLGMIWGDGSTDYNSALKSRLSISKDNSKSQVFLKMNSLQTDDTARYYCA---------------------    -
               SCOP domains d43cab_ B: Immunoglobulin heavy chain variable domain, VH                                                             SCOP domains
               CATH domains 43caB00 B:1-112 Immunoglobulins                                                                                       CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..........eeeeeeee......eeeeeeeee...eeeeeeee.....eee.......eeeeee....eeeeee...hhhhheeeeeeeee......eee...eee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------- Transcript
                43ca B    1 QVQLVESGPGLVAPSQSLSITCTVSGISLSRYNVHWVRQSPGKGLEWLGMIWGGGSIEYNPALKSRLSISKDNSKSQIFLKMNSLQTDDSAMYYCVSYGYGGDRFSYWGQGTLVTVS  112
                                    10        20        30        40        50        60        70        80  |||   87        97   ||  105       
                                                                                                            82A||               100A|            
                                                                                                             82B|                100B            
                                                                                                              82C

Chain C from PDB  Type:PROTEIN  Length:113
                                                                                                                                                  
               SCOP domains d43cac_ C: Immunoglobulin light chain kappa variable domain, VL-kappa                                             SCOP domains
               CATH domains 43caC00 C:1-107 Immunoglobulins                                                                                   CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee.............eeeeee......eeee.............eeeeee..eeeeee...hhhhheeeeeee...........eeeeee Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------- Transcript
                43ca C    1 DVVMTQTPSSLAMSVGQKVTMSCKSSQSLLNISNQKNYLAWYQQKPGQSPKLLVYFASTRESGVPDRFIGSGSGTDFTLTISSVQAEDQADYFCQQHYRAPRTFGGGTKLEIK  107
                                    10        20       27C|||     34        44        54        64        74        84        94       104   
                                                     27A|||||                                                                                
                                                      27B||||                                                                                
                                                       27C|||                                                                                
                                                        27D||                                                                                
                                                         27E|                                                                                
                                                          27F

Chain D from PDB  Type:PROTEIN  Length:117
 aligned with HVM44_MOUSE | P01820 from UniProtKB/Swiss-Prot  Length:115

    Alignment length:117
                                                                                                                         115                     
                                    29        39        49        59        69        79        89        99       109     |   -         -       
         HVM44_MOUSE     20 QVQLKESGPGLVAPSQSLSITCTVSGFSLTGYGVNWVRQPPGKGLEWLGMIWGDGSTDYNSALKSRLSISKDNSKSQVFLKMNSLQTDDTARYYCA---------------------    -
               SCOP domains d43cad_ D: Immunoglobulin heavy chain variable domain, VH                                                             SCOP domains
               CATH domains 43caD00 D:1-112 Immunoglobulins                                                                                       CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..........eeeeeeee......eeeeeeeee...eeeeeeee.....eeehhhhhh.eeeeee....eeeeee...hhhhheeeeeeeee......eee...eee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------- Transcript
                43ca D    1 QVQLVESGPGLVAPSQSLSITCTVSGISLSRYNVHWVRQSPGKGLEWLGMIWGGGSIEYNPALKSRLSISKDNSKSQIFLKMNSLQTDDSAMYYCVSYGYGGDRFSYWGQGTLVTVS  112
                                    10        20        30        40        50        60        70        80  |||   87        97   ||  105       
                                                                                                            82A||               100A|            
                                                                                                             82B|                100B            
                                                                                                              82C

Chain E from PDB  Type:PROTEIN  Length:113
                                                                                                                                                  
               SCOP domains d43cae_ E: Immunoglobulin light chain kappa variable domain, VL-kappa                                             SCOP domains
               CATH domains 43caE00 E:1-107 Immunoglobulins                                                                                   CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee.............eeeeee......eeee.............eeeeee..eeeeee........eeeeeee...........eeeeee Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------- Transcript
                43ca E    1 DVVMTQTPSSLAMSVGQKVTMSCKSSQSLLNISNQKNYLAWYQQKPGQSPKLLVYFASTRESGVPDRFIGSGSGTDFTLTISSVQAEDQADYFCQQHYRAPRTFGGGTKLEIK  107
                                    10        20       27C|||     34        44        54        64        74        84        94       104   
                                                     27A|||||                                                                                
                                                      27B||||                                                                                
                                                       27C|||                                                                                
                                                        27D||                                                                                
                                                         27E|                                                                                
                                                          27F

Chain F from PDB  Type:PROTEIN  Length:117
 aligned with HVM44_MOUSE | P01820 from UniProtKB/Swiss-Prot  Length:115

    Alignment length:117
                                                                                                                         115                     
                                    29        39        49        59        69        79        89        99       109     |   -         -       
         HVM44_MOUSE     20 QVQLKESGPGLVAPSQSLSITCTVSGFSLTGYGVNWVRQPPGKGLEWLGMIWGDGSTDYNSALKSRLSISKDNSKSQVFLKMNSLQTDDTARYYCA---------------------    -
               SCOP domains d43caf_ F: Immunoglobulin heavy chain variable domain, VH                                                             SCOP domains
               CATH domains 43caF00 F:1-112 Immunoglobulins                                                                                       CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..........eeeeeeee......eeeeeeeee...eeeeeeee.....eee.hhhhh.eeeeee....eeeeee...hhhhheeeeeeeee......eee...eee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------- Transcript
                43ca F    1 QVQLVESGPGLVAPSQSLSITCTVSGISLSRYNVHWVRQSPGKGLEWLGMIWGGGSIEYNPALKSRLSISKDNSKSQIFLKMNSLQTDDSAMYYCVSYGYGGDRFSYWGQGTLVTVS  112
                                    10        20        30        40        50        60        70        80  |||   87        97   ||  105       
                                                                                                            82A||               100A|            
                                                                                                             82B|                100B            
                                                                                                              82C

Chain G from PDB  Type:PROTEIN  Length:113
                                                                                                                                                  
               SCOP domains d43cag_ G: Immunoglobulin light chain kappa variable domain, VL-kappa                                             SCOP domains
               CATH domains 43caG00 G:1-107 Immunoglobulins                                                                                   CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee..eeeee....eeeeeee.............eeeeee......eeee.............eeeeee..eeeeee...hhhhheeeeeee...........eeeeee Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------- Transcript
                43ca G    1 DVVMTQTPSSLAMSVGQKVTMSCKSSQSLLNISNQKNYLAWYQQKPGQSPKLLVYFASTRESGVPDRFIGSGSGTDFTLTISSVQAEDQADYFCQQHYRAPRTFGGGTKLEIK  107
                                    10        20       27C|||     34        44        54        64        74        84        94       104   
                                                     27A|||||                                                                                
                                                      27B||||                                                                                
                                                       27C|||                                                                                
                                                        27D||                                                                                
                                                         27E|                                                                                
                                                          27F

Chain H from PDB  Type:PROTEIN  Length:117
 aligned with HVM44_MOUSE | P01820 from UniProtKB/Swiss-Prot  Length:115

    Alignment length:117
                                                                                                                         115                     
                                    29        39        49        59        69        79        89        99       109     |   -         -       
         HVM44_MOUSE     20 QVQLKESGPGLVAPSQSLSITCTVSGFSLTGYGVNWVRQPPGKGLEWLGMIWGDGSTDYNSALKSRLSISKDNSKSQVFLKMNSLQTDDTARYYCA---------------------    -
               SCOP domains d43cah_ H: Immunoglobulin heavy chain variable domain, VH                                                             SCOP domains
               CATH domains 43caH00 H:1-112 Immunoglobulins                                                                                       CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..........eeeeeeee.......eeeeeeee...eeeeeeee.....eeehhhhhh.eeeeee....eeeeee...hhhhheeeeeeee.......eee...eee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------- Transcript
                43ca H    1 QVQLVESGPGLVAPSQSLSITCTVSGISLSRYNVHWVRQSPGKGLEWLGMIWGGGSIEYNPALKSRLSISKDNSKSQIFLKMNSLQTDDSAMYYCVSYGYGGDRFSYWGQGTLVTVS  112
                                    10        20        30        40        50        60        70        80  |||   87        97   ||  105       
                                                                                                            82A||               100A|            
                                                                                                             82B|                100B            
                                                                                                              82C

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 '\|'

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Immunoglobulin-like (3897)

Homologous Superfamily: Immunoglobulins (2282)

House mouse (Mus musculus) (616)

1a	43caA00	A:1-107
1b	43caC00	C:1-107
1c	43caE00	E:1-107
1d	43caG00	G:1-107
1e	43caB00	B:1-112
1f	43caD00	D:1-112
1g	43caF00	F:1-112
1h	43caH00	H:1-112

(no "Pfam Domain" information available for 43CA)

Asymmetric Unit(hide GO term definitions)

Chain B,D,F,H (HVM44_MOUSE | P01820)

molecular function
	GO:0003823		antigen binding		Interacting selectively and non-covalently with an antigen, any substance which is capable of inducing a specific immune response and of reacting with the products of that response, the specific antibody or specifically sensitized T-lymphocytes, or both. Binding may counteract the biological activity of the antigen.

Asymmetric Unit
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	Cis Peptide Bonds
		Ala A:94 - Pro A:95	[ RasMol ]
		Ala C:94 - Pro C:95	[ RasMol ]
		Ala E:94 - Pro E:95	[ RasMol ]
		Ala G:94 - Pro G:95	[ RasMol ]
		Thr A:7 - Pro A:8	[ RasMol ]
		Thr C:7 - Pro C:8	[ RasMol ]
		Thr E:7 - Pro E:8	[ RasMol ]
		Thr G:7 - Pro G:8	[ RasMol ]

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	43ca
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(no "Related Entries Specified in the PDB File" available for 43CA)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 4)

Sites (8, 8)

SS Bonds (8, 8)

Cis Peptide Bonds (8, 8)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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SCOP Domains (2, 8)

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