1WCB - JenaLib

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Title :   PLP-DEPENDENT CATALYTIC ANTIBODY 15A9 IN COMPLEX WITH ITS HAPTEN

Authors :   B. Golinelli-Pimpaneau, P. Christen

Date :   12 Nov 04 (Deposition) - 03 Mar 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

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

Keywords :   Catalytic Antibody, Transamination, Pyridoxal-Phosphate, Hapten, Phosphopyridoxyl-L-Lysine, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   B. Golinelli-Pimpaneau, C. Luthi, P. Christen
Structural Basis For D-Amino Acid Transamination By The Pyridoxal- 5' -Phosphate - Dependent Catalytic Antibody 15A9.
J. Biol. Chem. V. 281 23969 2006
PubMed-ID: 16790434 | Reference-DOI: 10.1074/JBC.M602184200
(for further references see the PDB file header)

Molecule 1 - FAB FRAGMENT OF CATALYTIC ANTIBODY 15A9, LIGHT CHAIN
	Chains	:	A, L
	Engineered	:	YES
	Expression System	:	MUS MUSCULUS
	Expression System Cell Line	:	15A9 MURINE HYBRIDOMA
	Expression System Strain	:	BALB/C
	Expression System Taxid	:	10090
	Organism Common	:	MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090

Molecule 2 - FAB FRAGMENT OF CATALYTIC ANTIBODY 15A9, HEAVY CHAIN
	Chains	:	B, H
	Engineered	:	YES
	Expression System	:	MUS MUSCULUS
	Expression System Cell Line	:	15A9 MURINE HYBRIDOMA
	Expression System Strain	:	BALB/C
	Expression System Taxid	:	10090
	Organism Common	:	MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090

		1	2	3	4
Asymmetric Unit	:	A	B	H	L
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			H	L

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 11)

No.	Name	Count	Type	Full Name
1	IOD	9	Ligand/Ion	IODIDE ION
2	PE1	2	Ligand/Ion	N~2~-({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)-L-LYSINE

Biological Unit 1 (2, 5)

No.	Name	Count	Type	Full Name
1	IOD	4	Ligand/Ion	IODIDE ION
2	PE1	1	Ligand/Ion	N~2~-({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)-L-LYSINE

Biological Unit 2 (2, 6)

No.	Name	Count	Type	Full Name
1	IOD	5	Ligand/Ion	IODIDE ION
2	PE1	1	Ligand/Ion	N~2~-({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)-L-LYSINE

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	LYS B:96	BINDING SITE FOR RESIDUE IOD B1227
02	AC2	SOFTWARE	GLY B:97 , TYR B:99 , ASN B:100A , TRP B:100E	BINDING SITE FOR RESIDUE IOD B1228
03	AC3	SOFTWARE	ARG B:71	BINDING SITE FOR RESIDUE IOD B1229
04	AC4	SOFTWARE	GLY H:97 , TYR H:99 , ASN H:100A , TRP H:100E	BINDING SITE FOR RESIDUE IOD H1213
05	AC5	SOFTWARE	VAL A:206 , SER A:208 , ALA H:84	BINDING SITE FOR RESIDUE IOD H1214
06	AC6	SOFTWARE	ARG H:71	BINDING SITE FOR RESIDUE IOD H1215
07	AC7	SOFTWARE	LYS H:96	BINDING SITE FOR RESIDUE IOD H1216
08	AC8	SOFTWARE	GLU B:85 , SER L:191	BINDING SITE FOR RESIDUE IOD L1215
09	AC9	SOFTWARE	TYR A:32 , HIS A:34 , SER A:50 , ARG A:91 , SER A:92 , TYR A:94 , PHE A:96 , HOH A:2065 , HOH A:2121 , TYR B:33 , ARG B:52 , ASP B:95 , LYS B:96 , TYR B:100B , TRP B:100E , SER H:161 , HOH H:2100 , LYS L:169	BINDING SITE FOR RESIDUE PE1 A1215
10	BC1	SOFTWARE	LYS A:169 , SER B:161 , HOH B:2103 , TYR H:33 , ARG H:52 , ASP H:95 , TYR H:100B , TRP H:100E , TYR L:32 , HIS L:34 , SER L:50 , ARG L:91 , TYR L:94 , HOH L:2049 , HOH L:2105 , HOH L:2106 , HOH L:2107	BINDING SITE FOR RESIDUE PE1 L1216

Asymmetric Unit

No.	Residues
1	A:23	-	A:88
2	A:134	-	A:194
3	B:22	-	B:92
4	B:140	-	B:195
5	H:22	-	H:92
6	H:140	-	H:195
7	L:23	-	L:88
8	L:134	-	L:194

Asymmetric Unit

No.	Residues
1	Ser A:7	-	Pro A:8
2	Tyr A:94	-	Pro A:95
3	Tyr A:140	-	Pro A:141
4	Phe B:146	-	Pro B:147
5	Glu B:148	-	Pro B:149
6	Arg B:188	-	Pro B:189
7	Phe H:146	-	Pro H:147
8	Glu H:148	-	Pro H:149
9	Arg H:188	-	Pro H:189
10	Ser L:7	-	Pro L:8
11	Tyr L:94	-	Pro L:95
12	Tyr L:140	-	Pro L:141

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

(no "PROSITE Motif" information available for 1WCB)

(no "Exon" information available for 1WCB)

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:213
                                                                                                                                                                                                                                                      
               SCOP domains d1wcba1 A:1-107 automated matches                                                                         d1wcba2 A:108-214 automated matches                                                                         SCOP domains
               CATH domains 1wcbA01 A:1-108 Immunoglobulins                                                                            1wcbA02 A:109-214 Immunoglobulins                                                                          CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee.......eeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeee.......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhh...eeeeeee.......eeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1wcb A    1 DIELTQSPAIMAASPGEKVTITCSATSGVNYMHWFQQKPGTSPKLWIYSTSNLASAVPARFSGSGSGTSYSLTISRMEAEDAATYYCQQRSTYPFTFGGGTKLELKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC  214
                                    10        20      ||31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211   
                                                     27|                                                                                                                                                                                         
                                                      29

Chain B from PDB  Type:PROTEIN  Length:224
                                                                                                                                                                                                                                                                 
               SCOP domains d1wcbb1 B:1-113 Immunoglobulin heavy chain variable domain, VH                                                               d1wcbb2 B:114-214 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                     SCOP domains
               CATH domains 1wcbB01 B:1-113 Immunoglobulins                                                                                              1wcbB02 B:114-214 Immunoglobulins                                                                   CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee..hhh.eeeeeeee......eeeeee........eee.......eeeeee....eeeeee...hhhhheeeeeeeeee...hhhhh.......eeeee........eeeee........eeeeeeeeeee.....eeee.hhh....eee...ee....eeeeeeeeee.hhhhhh..eeeeeehhhheeeeee..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1wcb B    1 EVKLQESGGGLVQPGHSLRLSCATSGFTFTDYYMSWVRQPPGKALEWLGLIRNKANGYTKEYSASVKGRFTISRDNSQSILYLQMNALRAEDSATYYCVRDKGSYGNYEAWFAYWGQGTTVTVSSAKTTPPSVYPLAPGSQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSPRPSETVTCNVAHPASSTKVDKKIVPRD  214
                                    10        20        30        40        50  |||   57        67        77     |||84        94      100D||     108       118       128|      140       150       160       170       180       190       200       210    
                                                                              52A||                            82A||               100A|||||                         128|                                                                                   
                                                                               52B|                             82B|                100B||||                          131                                                                                   
                                                                                52C                              82C                 100C|||                                                                                                                
                                                                                                                                      100D||                                                                                                                
                                                                                                                                       100E|                                                                                                                
                                                                                                                                        100F

Chain H from PDB  Type:PROTEIN  Length:223
                                                                                                                                                                                                                                                                
               SCOP domains d1wcbh1 H:1-113 Immunoglobulin heavy chain variable domain, VH                                                               d1wcbh2 H:114-213 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                    SCOP domains
               CATH domains 1wcbH01 H:1-113 Immunoglobulins                                                                                              1wcbH02 H:114-213 Immunoglobulins                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..eee.....eeeeeeee..hhhhh.eeeeee......eeeeee.hhhhh..eee.......eeeeee....eeeeee...hhhhheeeeeee......hhhhh.......eeeee........eeeee........eeeeeeeeeee.....eeee.hhh....eee...ee....eeeeeeeeee.........eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1wcb H    1 EVKLQESGGGLVQPGHSLRLSCATSGFTFTDYYMSWVRQPPGKALEWLGLIRNKANGYTKEYSASVKGRFTISRDNSQSILYLQMNALRAEDSATYYCVRDKGSYGNYEAWFAYWGQGTTVTVSSAKTTPPSVYPLAPGSQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSPRPSETVTCNVAHPASSTKVDKKIVPR  213
                                    10        20        30        40        50  |||   57        67        77     |||84        94      100D||     108       118       128|      140       150       160       170       180       190       200       210   
                                                                              52A||                            82A||               100A|||||                         128|                                                                                  
                                                                               52B|                             82B|                100B||||                          131                                                                                  
                                                                                52C                              82C                 100C|||                                                                                                               
                                                                                                                                      100D||                                                                                                               
                                                                                                                                       100E|                                                                                                               
                                                                                                                                        100F

Chain L from PDB  Type:PROTEIN  Length:213
                                                                                                                                                                                                                                                      
               SCOP domains d1wcbl1 L:1-107 automated matches                                                                         d1wcbl2 L:108-214 automated matches                                                                         SCOP domains
               CATH domains 1wcbL01 L:1-108 Immunoglobulins                                                                            1wcbL02 L:109-214 Immunoglobulins                                                                          CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee.......eeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeee.......eeeee..hhhhhhh.eeeeeeeeeee......eeeee..eee...eeeee.........eeeeeeeeeehhhhhhh.eeeeee........eeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1wcb L    1 DIELTQSPAIMAASPGEKVTITCSATSGVNYMHWFQQKPGTSPKLWIYSTSNLASAVPARFSGSGSGTSYSLTISRMEAEDAATYYCQQRSTYPFTFGGGTKLELKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC  214
                                    10        20      ||31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211   
                                                     27|                                                                                                                                                                                         
                                                      29

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 '\|'

Asymmetric Unit

Classes(

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Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Immunoglobulin-like (3897)

Homologous Superfamily: Immunoglobulins (2282)

Mouse (Mus musculus) (152)

1a	1wcbA02	A:109-214
1b	1wcbL02	L:109-214
1c	1wcbA01	A:1-108
1d	1wcbL01	L:1-108
1e	1wcbB02	B:114-214
1f	1wcbH02	H:114-213
1g	1wcbB01	B:1-113
1h	1wcbH01	H:1-113

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

Asymmetric Unit(hide GO term definitions)

(no "Gene Ontology" information available for 1WCB)

Asymmetric Unit
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	Ligands, Modified Residues, Ions
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	Cis Peptide Bonds
		Arg B:188 - Pro B:189	[ RasMol ]
		Arg H:188 - Pro H:189	[ RasMol ]
		Glu B:148 - Pro B:149	[ RasMol ]
		Glu H:148 - Pro H:149	[ RasMol ]
		Phe B:146 - Pro B:147	[ RasMol ]
		Phe H:146 - Pro H:147	[ RasMol ]
		Ser A:7 - Pro A:8	[ RasMol ]
		Ser L:7 - Pro L:8	[ RasMol ]
		Tyr A:140 - Pro A:141	[ RasMol ]
		Tyr A:94 - Pro A:95	[ RasMol ]
		Tyr L:140 - Pro L:141	[ RasMol ]
		Tyr L:94 - Pro L:95	[ RasMol ]

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1wc7	FAB FRAGMENT OF PLP-DEPENDENT CATALYTIC ANTIBODY 15A9 IN COMPLEX WITH PHOSPHOPYRIDOXYL -L-ALANINE
2bmk	FAB FRAGMENT OF PLP-DEPENDENT CATALYTIC ANTIBODY 15A9 IN COMPLEX WITH PHOSPHOPYRIDOXYL -D-ALANINE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 11)

Sites (10, 10)

SS Bonds (8, 8)

Cis Peptide Bonds (12, 12)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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