1T4K - JenaLib

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Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF UNLIGANDED ALDOLASE ANTIBODY 93F3 FAB

Authors :   X. Zhu, I. A. Wilson

Date :   29 Apr 04 (Deposition) - 02 Nov 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

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

Keywords :   Enantioselectivity, Aldolase Antibody, Reactive Lysine, Aldol Reaction, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   X. Zhu, F. Tanaka, Y. Hu, A. Heine, R. Fuller, G. Zhong, A. J. Olson, R. A. Lerner, C. F. Barbas, I. A. Wilson
The Origin Of Enantioselectivity In Aldolase Antibodies: Crystal Structure, Site-Directed Mutagenesis, And Computational Analysis
J. Mol. Biol. V. 343 1269 2004
PubMed-ID: 15491612 | Reference-DOI: 10.1016/J.JMB.2004.08.102
(for further references see the PDB file header)

Molecule 1 - IMMUNOGLOBULIN IGG1, KAPPA LIGHT CHAIN
	Cell Line	:	93F3 MURINE HYBRIDOMA
	Chains	:	A, C
	Fragment	:	ANTIBODY FAB 93F3
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090

Molecule 2 - IMMUNOGLOBULIN IGG1, HEAVY CHAIN
	Cell Line	:	93F3 MURINE HYBRIDOMA
	Chains	:	B, D
	Fragment	:	ANTIBODY FAB 93F3
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			C	D
Biological Unit 3 (1x)	:	A (1x)	B (1x)	C (1x)	D (1x)
Biological Unit 4 (1x)	:	A (1x)	B (1x)	C (1x)	D (1x)

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 9)

No.	Name	Count	Type	Full Name
1	ZN	9	Ligand/Ion	ZINC ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 3 (0, 0)

No.	Name	Count	Type	Full Name
1	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 4 (0, 0)

No.	Name	Count	Type	Full Name
1	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN C:138 , ASP C:167 , HIS D:172 , HOH D:379	BINDING SITE FOR RESIDUE ZN C 301
2	AC2	SOFTWARE	GLU B:204 , ASP C:151 , HIS C:189	BINDING SITE FOR RESIDUE ZN C 302
3	AC3	SOFTWARE	ASP B:54 , HOH B:381 , ASP D:72	BINDING SITE FOR RESIDUE ZN B 303
4	AC4	SOFTWARE	GLU A:185 , HIS A:189 , HOH D:309	BINDING SITE FOR RESIDUE ZN A 304
5	AC5	SOFTWARE	ASN A:138 , ASP A:167 , ASP A:170 , HIS B:172	BINDING SITE FOR RESIDUE ZN A 305
6	AC6	SOFTWARE	ASN B:162 , SER B:165 , ARG C:155 , GLU C:185 , HIS C:189	BINDING SITE FOR RESIDUE ZN C 306
7	AC7	SOFTWARE	GLU A:187 , GLU D:204	BINDING SITE FOR RESIDUE ZN D 307
8	AC8	SOFTWARE	HIS B:83 , HOH B:336 , HIS D:83 , HOH D:384	BINDING SITE FOR RESIDUE ZN B 308
9	AC9	SOFTWARE	ASP B:72 , SER B:74 , ASP D:54 , HOH D:347	BINDING SITE FOR RESIDUE ZN B 309

Asymmetric Unit

No.	Residues
1	A:23	-	A:88
2	A:134	-	A:194
3	B:22	-	B:92
4	B:142	-	B:208
5	C:23	-	C:88
6	C:134	-	C:194
7	D:22	-	D:92
8	D:142	-	D:208

Asymmetric Unit

No.	Residues
1	Ser A:7	-	Pro A:8
2	Tyr A:140	-	Pro A:141
3	Phe B:148	-	Pro B:149
4	Glu B:150	-	Pro B:151
5	Arg B:200	-	Pro B:202
6	Ser C:7	-	Pro C:8
7	Tyr C:140	-	Pro C:141
8	Phe D:148	-	Pro D:149
9	Glu D:150	-	Pro D:151
10	Arg D:200	-	Pro D:202

(no "SAP(SNP)/Variant" information available for 1T4K)

Asymmetric Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	IG_MHC	PS00290	Immunoglobulins and major histocompatibility complex proteins signature.	IGKC_MOUSE	84-90	1	C:192-198

Biological Unit 1 (, 0)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	IG_MHC	PS00290	Immunoglobulins and major histocompatibility complex proteins signature.	IGKC_MOUSE	84-90	0	-

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	IG_MHC	PS00290	Immunoglobulins and major histocompatibility complex proteins signature.	IGKC_MOUSE	84-90	1	C:192-198

Biological Unit 3 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	IG_MHC	PS00290	Immunoglobulins and major histocompatibility complex proteins signature.	IGKC_MOUSE	84-90	1	C:192-198

Biological Unit 4 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	IG_MHC	PS00290	Immunoglobulins and major histocompatibility complex proteins signature.	IGKC_MOUSE	84-90	1	C:192-198

(no "Exon" information available for 1T4K)

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:217
                                                                                                                                                                                                                                                          
               SCOP domains d1t4ka1 A:1-107 Immunoglobulin light chain kappa variable domain, VL-kappa                                      d1t4ka2 A:108-212 Immunoglobulin light chain kappa constant domain, CL-kappa                              SCOP domains
               CATH domains 1t4kA01 A:1-108 Immunoglobulins                                                                                  1t4kA02 A:109-211 Immunoglobulins                                                                      - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee....ee....ee.eeeeee......eeeee...ee.......eeeeee..eeeeee........eeeeeee.....ee...eeeee.......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhh...eeeeeeee..eeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1t4k A    1 DIQMTQSPSSLAVSPGEKVTMSCRSSQSLFNSRTRKNYLAWYQQKPGQSPTKLIYWASTRESGVPDRFTGSGSGTDFTLTISSVQAEDLAIYYCKQSYDLPTFGAGTKLELKRSDAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRN  212
                                    10        20       27C|||     34        44        54        64        74        84        94||     105       115       125       135       145       155       165       175       185       195       205       
                                                     27A|||||                                                                  95|                                                                                                                   
                                                      27B||||                                                                   97                                                                                                                   
                                                       27C|||                                                                                                                                                                                        
                                                        27D||                                                                                                                                                                                        
                                                         27E|                                                                                                                                                                                        
                                                          27F

Chain B from PDB  Type:PROTEIN  Length:217
                                                                                                                                                                                                                                                          
               SCOP domains d1t4kb1 B:1-113 Immunoglobulin heavy chain variable domain, VH                                                       d1t4kb2 B:114-228 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                      SCOP domains
               CATH domains 1t4kB01 B:1-113 Immunoglobulins                                                                                      1t4kB02 B:114-228 Immunoglobulins                                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee.......eeeeeee......eeeeee.....eee.hhhh..eeeeee....eeeeee...hhhhheeeeeeee.......ee...eeeee........eeeee..........eeeeeeeeeee.....eeee.hhh....eee...ee....eeeeeeeeee.........eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1t4k B    1 EVMLVESGPGLVAPSQSLSITCTVSGFSLSDYGVSWIRQPPGKGLEWLGVIWGDGSTYYASALKFRLTISKDSSKSQVFLNMHSLQTDDSAMYYCAKHTYGGPGDSWGQGTSVTVSSASTTPPSVFPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSPRPSETVTCNVAHPASSTKVDKKIVPR  228
                                    10        20        30        40        50        60        70        80   |||  87        97   |   106       116       126   ||  138       148     ||163     ||174     ||186       196|||    209       219   ||  
                                                                                                             83A||              100A                           130|                  154|||    169|      180|          196|||                  223|  
                                                                                                              83B|                                              133                   156||     171       183           199||                   226  
                                                                                                               83C                                                                     157|                              200|                        
                                                                                                                                                                                        162                               202

Chain C from PDB  Type:PROTEIN  Length:217
 aligned with IGKC_MOUSE | P01837 from UniProtKB/Swiss-Prot  Length:106

    Alignment length:217
                                                                                                                                             1                                                                                                       
                                     -         -         -         -         -         -         -         -         -         -         -   |     7        17        27        37        47        57        67        77        87        97       
          IGKC_MOUSE      - -----------------------------------------------------------------------------------------------------------------ADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRN  104
               SCOP domains d1t4kc1 C:1-107 Immunoglobulin light chain kappa variable domain, VL-kappa                                      d1t4kc2 C:108-212 Immunoglobulin light chain kappa constant domain, CL-kappa                              SCOP domains
               CATH domains 1t4kC01 C:1-108 Immunoglobulins                                                                                  1t4kC02 C:109-211 Immunoglobulins                                                                      - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee....ee....ee.eeeeee......eeeee...ee.......eeeeee..eeeeee........eeeeeee.....ee...eeeee.......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhh...eeeeeeee..eeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------IG_MHC -------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1t4k C    1 DIQMTQSPSSLAVSPGEKVTMSCRSSQSLFNSRTRKNYLAWYQQKPGQSPTKLIYWASTRESGVPDRFTGSGSGTDFTLTISSVQAEDLAIYYCKQSYDLPTFGAGTKLELKRSDAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRN  212
                                    10        20       27C|||     34        44        54        64        74        84        94||     105       115       125       135       145       155       165       175       185       195       205       
                                                     27A|||||                                                                  95|                                                                                                                   
                                                      27B||||                                                                   97                                                                                                                   
                                                       27C|||                                                                                                                                                                                        
                                                        27D||                                                                                                                                                                                        
                                                         27E|                                                                                                                                                                                        
                                                          27F

Chain D from PDB  Type:PROTEIN  Length:217
                                                                                                                                                                                                                                                          
               SCOP domains d1t4kd1 D:1-113 Immunoglobulin heavy chain variable domain, VH                                                       d1t4kd2 D:114-228 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                      SCOP domains
               CATH domains 1t4kD01 D:1-113 Immunoglobulins                                                                                      1t4kD02 D:114-228 Immunoglobulins                                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee.......eeeeeee......eeeeee.....eee.hhhh..eeeeee....eeeeee...hhhhheeeeeeee.......ee...eeeee........eeeee..........eeeeeeeeeee.....eeee.hhh....eee...eee..eeeeeeeeeee.........eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1t4k D    1 EVMLVESGPGLVAPSQSLSITCTVSGFSLSDYGVSWIRQPPGKGLEWLGVIWGDGSTYYASALKFRLTISKDSSKSQVFLNMHSLQTDDSAMYYCAKHTYGGPGDSWGQGTSVTVSSASTTPPSVFPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSPRPSETVTCNVAHPASSTKVDKKIVPR  228
                                    10        20        30        40        50        60        70        80   |||  87        97   |   106       116       126   ||  138       148     ||163     ||174     ||186       196|||    209       219   ||  
                                                                                                             83A||              100A                           130|                  154|||    169|      180|          196|||                  223|  
                                                                                                              83B|                                              133                   156||     171       183           199||                   226  
                                                                                                               83C                                                                     157|                              200|                        
                                                                                                                                                                                        162                               202

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	1t4kA02	A:109-211
1b	1t4kB02	B:114-228
1c	1t4kD02	D:114-228
1d	1t4kA01	A:1-108
1e	1t4kC01	C:1-108
1f	1t4kB01	B:1-113
1g	1t4kD01	D:1-113
1h	1t4kC02	C:109-211

(no "Pfam Domain" information available for 1T4K)

Asymmetric Unit(hide GO term definitions)

Chain C (IGKC_MOUSE | P01837)

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.
	GO:0034987	immunoglobulin receptor binding	Interacting selectively and non-covalently with one or more specific sites on an immunoglobulin receptor molecule.
biological process
	GO:0030183	B cell differentiation	The process in which a precursor cell type acquires the specialized features of a B cell. A B cell is a lymphocyte of B lineage with the phenotype CD19-positive and capable of B cell mediated immunity.
	GO:0050853	B cell receptor signaling pathway	A series of molecular signals initiated by the cross-linking of an antigen receptor on a B cell.
	GO:0006958	complement activation, classical pathway	Any process involved in the activation of any of the steps of the classical pathway of the complement cascade which allows for the direct killing of microbes, the disposal of immune complexes, and the regulation of other immune processes.
	GO:0042742	defense response to bacterium	Reactions triggered in response to the presence of a bacterium that act to protect the cell or organism.
	GO:0045087	innate immune response	Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
	GO:0006911	phagocytosis, engulfment	The internalization of bacteria, immune complexes and other particulate matter or of an apoptotic cell by phagocytosis, including the membrane and cytoskeletal processes required, which involves one of three mechanisms: zippering of pseudopods around a target via repeated receptor-ligand interactions, sinking of the target directly into plasma membrane of the phagocytosing cell, or induced uptake via an enhanced membrane ruffling of the phagocytosing cell similar to macropinocytosis.
	GO:0006910	phagocytosis, recognition	The initial step in phagocytosis involving adhesion to bacteria, immune complexes and other particulate matter, or an apoptotic cell and based on recognition of factors such as bacterial cell wall components, opsonins like complement and antibody or protein receptors and lipids like phosphatidyl serine, and leading to intracellular signaling in the phagocytosing cell.
	GO:0050871	positive regulation of B cell activation	Any process that activates or increases the frequency, rate or extent of B cell activation.
cellular component
	GO:0072562	blood microparticle	A phospholipid microvesicle that is derived from any of several cell types, such as platelets, blood cells, endothelial cells, or others, and contains membrane receptors as well as other proteins characteristic of the parental cell. Microparticles are heterogeneous in size, and are characterized as microvesicles free of nucleic acids.
	GO:0009897	external side of plasma membrane	The leaflet of the plasma membrane that faces away from the cytoplasm and any proteins embedded or anchored in it or attached to its surface.
	GO:0042571	immunoglobulin complex, circulating	An immunoglobulin complex that is secreted into extracellular space and found in mucosal areas or other tissues or circulating in the blood or lymph. In its canonical form, a circulating immunoglobulin complex is composed of two identical heavy chains and two identical light chains, held together by disulfide bonds. Some forms of are polymers of the basic structure and contain additional components such as J-chain and the secretory component.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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	1t4k
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Description

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Ligands, Modified Residues, Ions (1, 9)

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SS Bonds (8, 8)

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