1WC7 - JenaLib

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

Authors :   B. Golinelli-Pimpaneau, P. Christen

Date :   09 Nov 04 (Deposition) - 30 Nov 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.33

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

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

Reference :   B. Golinelli-Pimpaneau
Structure Of A Pseudomerohedrally Twinned Monoclinic Crystal Form Of A Pyridoxal Phosphate-Dependent Catalytic Antibody
Acta Crystallogr. , Sect. D V. 61 472 2005
PubMed-ID: 15805602 | Reference-DOI: 10.1107/S0907444905003331
(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, 6)

No.	Name	Count	Type	Full Name
1	IOD	5	Ligand/Ion	IODIDE ION
2	PP3	1	Ligand/Ion	ALANYL-PYRIDOXAL-5'-PHOSPHATE

Biological Unit 1 (2, 3)

No.	Name	Count	Type	Full Name
1	IOD	2	Ligand/Ion	IODIDE ION
2	PP3	1	Ligand/Ion	ALANYL-PYRIDOXAL-5'-PHOSPHATE

Biological Unit 2 (1, 3)

No.	Name	Count	Type	Full Name
1	IOD	3	Ligand/Ion	IODIDE ION
2	PP3	-1	Ligand/Ion	ALANYL-PYRIDOXAL-5'-PHOSPHATE

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:61 , THR H:68 , ASN H:82A	BINDING SITE FOR RESIDUE IOD A1213
2	AC2	SOFTWARE	GLY B:97 , ASN B:100A , TRP B:100E	BINDING SITE FOR RESIDUE IOD B1214
3	AC3	SOFTWARE	GLY H:97 , ASN H:100A , TRP H:100E	BINDING SITE FOR RESIDUE IOD H1214
4	AC4	SOFTWARE	TYR H:33 , ARG H:52 , TYR L:94	BINDING SITE FOR RESIDUE IOD H1215
5	AC5	SOFTWARE	THR B:68 , ASN B:82A	BINDING SITE FOR RESIDUE IOD L1213
6	AC6	SOFTWARE	ASN A:31 , 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	BINDING SITE FOR RESIDUE PP3 A1214

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: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 1WC7)

(no "PROSITE Motif" information available for 1WC7)

(no "Exon" information available for 1WC7)

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 d1wc7a1 A:1-107 automated matches                                                                         d1wc7a2 A:108-214 automated matches                                                                         SCOP domains
               CATH domains 1wc7A01 A:1-108 Immunoglobulins                                                                            1wc7A02 A:109-214 Immunoglobulins                                                                          CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee.......eeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeee............eeeee.......ee.....hhhhhhh...ee..eeeee.....eeeeee..eee...ee............eeee.eee.hhhhhh.....eeeee.......eeee...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1wc7 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 d1wc7b1 B:1-113 Immunoglobulin heavy chain variable domain, VH                                                               d1wc7b2 B:114-211 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                 --- SCOP domains
               CATH domains 1wc7B01 B:1-113 Immunoglobulins                                                                                              1wc7B02 B:114-214 Immunoglobulins                                                                   CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee.....ee.....eee..eee..hhh.eeeeeeee......eeee...hhhhh.....hhhhh..eeeeee....eeeeee...hhhhheeeeeeeeee...............eeeee........eeeee...........eeeeeeee.....eeee........eee...ee....eeeeeee............eeeeee....eeeeee..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1wc7 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:224
                                                                                                                                                                                                                                                                 
               SCOP domains d1wc7h1 H:1-113 Immunoglobulin heavy chain variable domain, VH                                                               d1wc7h2 H:114-214 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                     SCOP domains
               CATH domains 1wc7H01 H:1-113 Immunoglobulins                                                                                              1wc7H02 H:114-212 Immunoglobulins                                                                -- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee....eee.....eee..eee..hhh.eeeeeeee......eeeeee.hhhhh..eee.......eeee........eeee...hhhhheeeeeeeeee...............eeeee........eeeee........eeeeeeeeeee.....eeee.hhh....eee...ee....eeeeeeeeee.........eeeeee....eeeeee..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1wc7 H    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 L from PDB  Type:PROTEIN  Length:212
                                                                                                                                                                                                                                                     
               SCOP domains d1wc7l1 L:1-107 automated matches                                                                         d1wc7l2 L:108-213 automated matches                                                                        SCOP domains
               CATH domains 1wc7L01 L:1-108 Immunoglobulins                                                                            1wc7L02 L:109-210 Immunoglobulins                                                                     --- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee.......eeeee......eeeee...ee.......eeeeee..eeeeee...hhhhh.eeeee............eeeee.......eeeee..hhhhhh....eeeeeee......eeeeeee........ee.................eee.hhhhhhh..eeeeeeee......eeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1wc7 L    1 DIELTQSPAIMAASPGEKVTITCSATSGVNYMHWFQQKPGTSPKLWIYSTSNLASAVPARFSGSGSGTSYSLTISRMEAEDAATYYCQQRSTYPFTFGGGTKLELKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNE  213
                                    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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Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Immunoglobulin-like (3897)

Homologous Superfamily: Immunoglobulins (2282)

Mouse (Mus musculus) (152)

1a	1wc7A02	A:109-214
1b	1wc7L02	L:109-210
1c	1wc7A01	A:1-108
1d	1wc7L01	L:1-108
1e	1wc7B02	B:114-214
1f	1wc7H02	H:114-212
1g	1wc7B01	B:1-113
1h	1wc7H01	H:1-113

(no "Pfam Domain" information available for 1WC7)

Asymmetric Unit(hide GO term definitions)

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		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
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 6)

Sites (6, 6)

SS Bonds (7, 7)

Cis Peptide Bonds (12, 12)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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