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Asym./Biol. Unit (Jmol Viewer)

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Title :   CATIONIC CYCLIZATION ANTIBODY 4C6 IN COMPLEX WITH BENZOIC ACID

Authors :   X. Zhu, I. A. Wilson

Date :   05 Dec 02 (Deposition) - 13 May 03 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.30

Chains :   Asym./Biol. Unit : H,L

Keywords :   Immunoglobulin, Catalytic Antibody, Cationic Cyclization Reaction, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   X. Zhu, A. Heine, F. Monnat, K. N. Houk, K. D. Janda, I. A. Wilson
Structural Basis For Antibody Catalysis Of A Cationic Cyclization Reaction
J. Mol. Biol. V. 329 69 2003
PubMed-ID: 12742019 | Reference-DOI: 10.1016/S0022-2836(03)00406-6

Molecule 1 - IMMUNOGLOBULIN IGG2A
	Chains	:	L
	Fragment	:	ANTIBODY FAB FRAGMENT 4C6, LIGHT CHAIN
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Other Details	:	PURIFIED FROM ASCITIC FLUID
	Strain	:	129G1X+

Molecule 2 - IMMUNOGLOBULIN IGG2A
	Chains	:	H
	Fragment	:	ANTIBODY FAB FRAGMENT 4C6, HEAVY CHAIN
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Other Details	:	PURIFIED FROM ASCITIC FLUID
	Strain	:	129G1X+

		1	2
Asymmetric/Biological Unit	:	H	L

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 5)

No.	Name	Count	Type	Full Name
1	BEZ	1	Ligand/Ion	BENZOIC ACID
2	GOL	4	Ligand/Ion	GLYCEROL

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ALA H:34 , ASN H:35A , LEU H:95 , PRO H:230 , TRP L:89 , GLY L:91	BINDING SITE FOR RESIDUE BEZ H 601
2	AC2	SOFTWARE	PHE H:174 , PRO H:175 , THR H:186 , LEU H:187 , SER H:188 , HOH H:685 , HOH H:733 , SER L:162 , SER L:176 , THR L:178	BINDING SITE FOR RESIDUE GOL H 611
3	AC3	SOFTWARE	VAL H:12 , GLN H:16 , SER H:17 , ASP H:32 , TYR H:53 , HOH H:621 , HOH H:653 , HOH H:686 , HOH H:806	BINDING SITE FOR RESIDUE GOL H 612
4	AC4	SOFTWARE	SER H:120 , VAL H:121 , SER H:215 , VAL H:219 , LYS H:221 , HOH H:668 , HOH H:709 , GLU L:123	BINDING SITE FOR RESIDUE GOL H 613
5	AC5	SOFTWARE	ARG H:71 , ASP H:72 , THR H:73 , LYS L:53 , LEU L:54 , HOH L:236	BINDING SITE FOR RESIDUE GOL H 614

Asymmetric/Biological Unit

No.	Residues
1	H:22	-	H:92
2	H:142	-	H:208
3	L:23	-	L:88
4	L:134	-	L:194
5	L:214	-	H:128

Asymmetric/Biological Unit

No.	Residues
1	Ser L:7	-	Pro L:8
2	Phe L:94	-	Pro L:95
3	Tyr L:140	-	Pro L:141
4	Phe H:148	-	Pro H:149
5	Glu H:150	-	Pro H:151
6	Trp H:199	-	Pro H:200

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

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

(no "Exon" information available for 1NCW)

Asymmetric/Biological 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 H from PDB  Type:PROTEIN  Length:222
                                                                                                                                                                                                                                                               
               SCOP domains d1ncwh1 H:1-113 Immunoglobulin heavy chain variable domain, VH                                                         d1ncwh2 H:114-231 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                         SCOP domains
               CATH domains 1ncwH01 H:1-113 Immunoglobulins                                                                                        1ncwH02 H:114-227 Immunoglobulins                                                                  ---- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee.......eeeeeeeee...eeeeeeeee....eee.hhhh..eeeeee....eeeeee...hhhhheeeeeeeee.......ee...eeeee........eeeee..hhhhh...eeeeeeeeeee.....eeee.hhh....eee...eee..eeeeeeeeeee.hhh.....eeeeeehhhheeeeee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                1ncw H    1 RVQLQQSGPGLVKPSQSLSLTCTVTGYSITSDFAWNWIRQFPGNKLEWMGYINYSGFTSHNPSLKSRISITRDTSKNQFFLQLNSVTTEDTATYYCAGLLWYDGGAGSWGQGTLVTVSAAKTTAPSVYPLAPVCGDTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEPRGPT  231
                                    10        20        30     |  39        49        59        69        79   |||  86        96    || 104       114       124     ||136       146       157|      172       184       194 || || 206|      217     ||229  
                                                             35A                                             82A||               100A|                           130|                  154|||    169|      180|          196| || 206|            223|     
                                                                                                              82B|                100B                            133                   156||     171       183           198 ||  208             226     
                                                                                                               82C                                                                       157|                               200|                          
                                                                                                                                                                                          162                                202

Chain L from PDB  Type:PROTEIN  Length:219
 aligned with Q58EU8_MOUSE | Q58EU8 from UniProtKB/TrEMBL  Length:239

    Alignment length:219
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230         
        Q58EU8_MOUSE     21 DVVMTQTPLTLSVTIGQPASISCKSSQSLLHSNGKTYLNWLLQRPGQSPKLLIYLVSKLESGVPDRFSGSGSGTDFTLKISRVEAEDLGVYYCLQATHFPRTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC  239
               SCOP domains d1ncwl1 L:1-107 Immunoglobulin light chain kappa variable domain, VL-kappa                                      d1ncwl2 L:108-214 Immunoglobulin light chain kappa constant domain, CL-kappa                                SCOP domains
               CATH domains 1ncwL01 L:1-108 Immunoglobulins                                                                                  1ncwL02 L:109-214 Immunoglobulins                                                                          CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee............eeeeee.....eeeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeeee......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhhhh.eeeeeee.......eeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1ncw L    1 DVVMTQSPKTISVTIGQPASISCKSSQRLLNSNGKTFLNWLLQRPGQSPKRLIYLGTKLDSGVPDRFTGSGSGTDFTLKISRVEAEDLGVYYCWQGTHFPYTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC  214
                                    10        20       27C||      35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205         
                                                     27A||||                                                                                                                                                                                           
                                                      27B|||                                                                                                                                                                                           
                                                       27C||                                                                                                                                                                                           
                                                        27D|                                                                                                                                                                                           
                                                         27E

Legend:		→ Mismatch	(orange background)
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		→ 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/Biological 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	1ncwL02	L:109-214
1b	1ncwL01	L:1-108
1c	1ncwH02	H:114-227
1d	1ncwH01	H:1-113

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

Asymmetric/Biological Unit(hide GO term definitions)

Chain L (Q58EU8_MOUSE | Q58EU8)

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Glu H:150 - Pro H:151	[ RasMol ]
		Phe H:148 - Pro H:149	[ RasMol ]
		Phe L:94 - Pro L:95	[ RasMol ]
		Ser L:7 - Pro L:8	[ RasMol ]
		Trp H:199 - Pro H:200	[ RasMol ]
		Tyr L:140 - Pro L:141	[ RasMol ]

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1nd0	CATIONIC CYCLIZATION ANTIBODY 4C6 COMPLEX WITH TRANSITION STATE ANALOG

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 5)

Sites (5, 5)

SS Bonds (5, 5)

Cis Peptide Bonds (6, 6)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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SCOP Domains (4, 4)

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