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Title :   FAB FRAGMENT OF PLP-DEPENDENT CATALYTIC ANTIBODY 15A9 IN COMPLEX WITH PHOSPHOPYRIDOXYL-D-ALANINE

Authors :   B. Golinelli-Pimpaneau, P. Christen

Date :   14 Mar 05 (Deposition) - 03 Mar 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

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, 8)

No.	Name	Count	Type	Full Name
1	IOD	6	Ligand/Ion	IODIDE ION
2	PDD	2	Ligand/Ion	N-(5'-PHOSPHOPYRIDOXYL)-D-ALANINE

Biological Unit 1 (2, 4)

No.	Name	Count	Type	Full Name
1	IOD	3	Ligand/Ion	IODIDE ION
2	PDD	1	Ligand/Ion	N-(5'-PHOSPHOPYRIDOXYL)-D-ALANINE

Biological Unit 2 (2, 4)

No.	Name	Count	Type	Full Name
1	IOD	3	Ligand/Ion	IODIDE ION
2	PDD	1	Ligand/Ion	N-(5'-PHOSPHOPYRIDOXYL)-D-ALANINE

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TYR B:32 , GLY B:97 , TYR B:99 , TRP B:100E	BINDING SITE FOR RESIDUE IOD B1215
2	AC2	SOFTWARE	ASN B:52A , ASN B:53	BINDING SITE FOR RESIDUE IOD B1216
3	AC3	SOFTWARE	THR B:68	BINDING SITE FOR RESIDUE IOD B1218
4	AC4	SOFTWARE	THR H:68 , ASN H:82A	BINDING SITE FOR RESIDUE IOD H1215
5	AC5	SOFTWARE	GLY H:97 , TYR H:99 , ASN H:100A , TRP H:100E	BINDING SITE FOR RESIDUE IOD H1216
6	AC6	SOFTWARE	GLY H:26 , PHE H:27	BINDING SITE FOR RESIDUE IOD H1217
7	AC7	SOFTWARE	TYR A:32 , HIS A:34 , ARG A:91 , SER A:92 , TYR A:94 , TYR B:33 , ARG B:52 , ASP B:95 , LYS B:96 , HOH B:2080 , HOH B:2081 , HOH B:2082	BINDING SITE FOR RESIDUE PDD B1217
8	AC8	SOFTWARE	TYR H:33 , ARG H:52 , ASP H:95 , TYR L:32 , HIS L:34 , ARG L:91 , SER L:92 , TYR L:94 , HOH L:2096 , HOH L:2097	BINDING SITE FOR RESIDUE PDD L1215

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 2BMK)

(no "PROSITE Motif" information available for 2BMK)

(no "Exon" information available for 2BMK)

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 d2bmka1 A:1-107 automated matches                                                                         d2bmka2 A:108-214 automated matches                                                                         SCOP domains
               CATH domains 2bmkA01 A:1-108 Immunoglobulins                                                                            2bmkA02 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..hhhhhhh.eeeeeeeeeee....eeeeeee..eee...eeeee.........eeeeeeeeeehhhhh...eeeeeeee......eeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2bmk 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 d2bmkb1 B:1-113 Immunoglobulin heavy chain variable domain, VH                                                               d2bmkb2 B:114-214 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                     SCOP domains
               CATH domains 2bmkB01 B:1-113 Immunoglobulins                                                                                              2bmkB02 B:114-214 Immunoglobulins                                                                   CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee..hhh.eeeeeeee......eeeeee.hhhhh..eee.......eeeeee....eeeeee...hhhhheeeeeeeeee...hhhhh..ee...eeeee........eeeee........eeeeeeeeeee.....eeee.hhh....eee...eee..eeeeeeeeeee.........eeeeeehhhheeeeee..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2bmk 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:222
                                                                                                                                                                                                                                                               
               SCOP domains d2bmkh1 H:1-113 Immunoglobulin heavy chain variable domain, VH                                                               d2bmkh2 H:114-214 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                   SCOP domains
               CATH domains 2bmkH01 H:1-113 Immunoglobulins                                                                                              2bmkH02 H:114-214 Immunoglobulins                                                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeee..eee.....eeeeeeee..hhhhh.eeeeee......eeeeee........eee.hhhh..eeeeee....eeeeee...hhhhheeeeeee......hhhhh..ee...eeeee........eeeee......eeeeeeeeeee.....eeee.hhh....eee...eee..eeeeeeeeeee.........eeeeeehhhheeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                2bmk H    1 EVKLQESGGGLVQPGHSLRLSCATSGFTFTDYYMSWVRQPPGKALEWLGLIRNKANGYTKEYSASVKGRFTISRDNSQSILYLQMNALRAEDSATYYCVRDKGSYGNYEAWFAYWGQGTTVTVSSAKTTPPSVYPLAPGSNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSPRPSETVTCNVAHPASSTKVDKKIVPRD  214
                                    10        20        30        40        50  |||   57        67        77     |||84        94      100D||     108       118       128|      142       152       162       172       182       192       202       212  
                                                                              52A||                            82A||               100A|||||                         128|                                                                                 
                                                                               52B|                             82B|                100B||||                          133                                                                                 
                                                                                52C                              82C                 100C|||                                                                                                              
                                                                                                                                      100D||                                                                                                              
                                                                                                                                       100E|                                                                                                              
                                                                                                                                        100F

Chain L from PDB  Type:PROTEIN  Length:213
                                                                                                                                                                                                                                                      
               SCOP domains d2bmkl1 L:1-107 automated matches                                                                         d2bmkl2 L:108-214 automated matches                                                                         SCOP domains
               CATH domains 2bmkL01 L:1-108 Immunoglobulins                                                                            2bmkL02 L:109-214 Immunoglobulins                                                                          CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeeeeeee...eeeee......eeeee...ee.......eeeeeeeeeeeeee...hhhhheeeeeee......ee...eeeee.......eeeee..hhhhhhhheeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhh...eeeeeee.......eeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2bmk 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

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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( (-)

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Topologies( (-)

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Homologous Superfamilies( (-)

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Organisms( (-)

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Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Immunoglobulin-like (3897)

Homologous Superfamily: Immunoglobulins (2282)

Mouse (Mus musculus) (152)

1a	2bmkA02	A:109-214
1b	2bmkL02	L:109-214
1c	2bmkA01	A:1-108
1d	2bmkL01	L:1-108
1e	2bmkB02	B:114-214
1f	2bmkH02	H:114-214
1g	2bmkB01	B:1-113
1h	2bmkH01	H:1-113

(no "Pfam Domain" information available for 2BMK)

Asymmetric Unit(hide GO term definitions)

(no "Gene Ontology" information available for 2BMK)

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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
1wcb	PLP-DEPENDENT CATALYTIC ANTIBODY 15A9 IN COMPLEX WITH ITS HAPTEN

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 8)

Sites (8, 8)

SS Bonds (8, 8)

Cis Peptide Bonds (12, 12)

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