1KN2 - JenaLib

Asym.Unit - manually (Jmol Viewer)

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Title :   CATALYTIC ANTIBODY D2.3 COMPLEX

Authors :   B. Gigant, M. Knossow

Date :   18 Dec 01 (Deposition) - 13 Mar 02 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

Chains :   Asym. Unit : H,L
Biol. Unit 1: H,L  (1x)
Biol. Unit 2: H,L  (2x)
Biol. Unit 3: H (2x),L (2x)
Biol. Unit 4: H (1x),L (1x)

Keywords :   Abzyme, Transition State Analog, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   L. J. D'Souza, B. Gigant, M. Knossow, B. S. Green
Remarkable Remote Chiral Recognition In A Reaction Mediated By A Catalytic Antibody.
J. Am. Chem. Soc. V. 124 2114 2002
PubMed-ID: 11878955 | Reference-DOI: 10.1021/JA0170504
(for further references see the PDB file header)

Molecule 1 - IG ANTIBODY D2.3 (LIGHT CHAIN)
	Chains	:	L
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090

Molecule 2 - IG ANTIBODY D2.3 (HEAVY CHAIN)
	Chains	:	H
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 8)

No.	Name	Count	Type	Full Name
1	PNE	1	Ligand/Ion	PARA-NITROPHENYL PHOSPHONOBUTANOYL L-ALANINE
2	ZN	7	Ligand/Ion	ZINC ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	PNE	1	Ligand/Ion	PARA-NITROPHENYL PHOSPHONOBUTANOYL L-ALANINE
2	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (1, 2)

No.	Name	Count	Type	Full Name
1	PNE	2	Ligand/Ion	PARA-NITROPHENYL PHOSPHONOBUTANOYL L-ALANINE
2	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 3 (1, 2)

No.	Name	Count	Type	Full Name
1	PNE	2	Ligand/Ion	PARA-NITROPHENYL PHOSPHONOBUTANOYL L-ALANINE
2	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 4 (1, 1)

No.	Name	Count	Type	Full Name
1	PNE	1	Ligand/Ion	PARA-NITROPHENYL PHOSPHONOBUTANOYL L-ALANINE
2	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP H:100C , HIS L:49 , LYS L:53 , HOH L:581	BINDING SITE FOR RESIDUE ZN L 553
2	AC2	SOFTWARE	ASP H:181 , HIS L:93 , ZN L:559 , HOH L:561 , HOH L:571	BINDING SITE FOR RESIDUE ZN L 554
3	AC3	SOFTWARE	ASP L:151 , HIS L:189 , ZN L:557 , ZN L:558 , HOH L:601 , HOH L:602	BINDING SITE FOR RESIDUE ZN L 555
4	AC4	SOFTWARE	ASP L:60 , ZN L:557 , ZN L:558 , HOH L:560 , HOH L:603 , HOH L:619	BINDING SITE FOR RESIDUE ZN L 556
5	AC5	SOFTWARE	ZN L:555 , ZN L:556 , HOH L:602 , HOH L:603	BINDING SITE FOR RESIDUE ZN L 557
6	AC6	SOFTWARE	ZN L:555 , ZN L:556 , HOH L:601 , HOH L:612 , HOH L:619 , HOH L:635	BINDING SITE FOR RESIDUE ZN L 558
7	AC7	SOFTWARE	SER H:112 , ZN L:554 , HOH L:571 , HOH L:620	BINDING SITE FOR RESIDUE ZN L 559
8	AC8	SOFTWARE	HIS H:35 , VAL H:37 , TRP H:47 , ARG H:50 , TRP H:95 , PHE H:97 , TYR H:100D , TYR L:27D , ASN L:34 , VAL L:89 , GLY L:91 , TYR L:96 , PHE L:98 , HOH L:562	BINDING SITE FOR RESIDUE PNE L 551

Asymmetric Unit

No.	Residues
1	H:22	-	H:92
2	H:140	-	H:206
3	L:23	-	L:88
4	L:134	-	L:194

Asymmetric 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:146	-	Pro H:147
5	Glu H:148	-	Pro H:149
6	Trp H:197	-	Pro H:198

(no "SAP(SNP)/Variant" information available for 1KN2)

(no "PROSITE Motif" information available for 1KN2)

(no "Exon" information available for 1KN2)

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 H from PDB  Type:PROTEIN  Length:222
                                                                                                                                                                                                                                                               
               SCOP domains d1kn2h1 H:1-113 Immunoglobulin heavy chain variable domain, VH                                                             d1kn2h2 H:114-223 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                     SCOP domains
               CATH domains 1kn2H01 H:1-113 Immunoglobulins                                                                                            1kn2H02 H:114-223 Immunoglobulins                                                                   CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee..hhhhh.eeeeee.....eeeeeee......eee.hhhh..eeeeee....eeeeee...hhhhheeeeeee.............ee...eeeee........eeeee..........eeeeeeeeeee.....eeee.hhh....eee...eee..eeeeeeeeeee.........eeeeeehhhheeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                1kn2 H    1 EMQLQQSGAELLRPGTSVKLSCKTSGYIFTSYWIHWVKQRSGQGLEWIARIYPGTGSTYYNEKFKGKATLTADKSSSTAYMQLSTLKSEDSAVYFCTRWGFIPVREDYVMDYWGQGTLVTVSSAKTTAPSVYPLAPVCGDTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEP  223
                                    10        20        30        40        50  |     59        69        79   |||  86        96    ||100F       110       120       130       140       150 ||||  165 ||    176 ||    188     ||200   ||  211       221  
                                                                              52A                            82A||               100A|||||                                                 152|||    167|      178|          194| || 204|                 
                                                                                                              82B|                100B||||                                                  154||     169       181           196 ||  206                 
                                                                                                               82C                 100C|||                                                   155|                               198|                      
                                                                                                                                    100D||                                                    160                                200                      
                                                                                                                                     100E|                                                                                                                
                                                                                                                                      100F

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 d1kn2l1 L:1-107 Immunoglobulin light chain kappa variable domain, VL-kappa                                      d1kn2l2 L:108-214 Immunoglobulin light chain kappa constant domain, CL-kappa                                SCOP domains
               CATH domains 1kn2L01 L:1-108 Immunoglobulins                                                                                  1kn2L02 L:109-214 Immunoglobulins                                                                          CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee............eeeeee.....eeeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeee.......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhh...eeeeeee.......eeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1kn2 L    1 DIVMTQSPLTLSVTIGQPASISCKSSQSLLYSNGKTYLNWLLQRPGQSPKRLIHLVSKLDSGVPDRITGSGSGTDFTLKISRVEAADLGVYYCVQGTHFPYTFGGGTKLEILRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC  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)
	-	→ 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	1kn2L02	L:109-214
1b	1kn2L01	L:1-108
1c	1kn2H02	H:114-223
1d	1kn2H01	H:1-113

(no "Pfam Domain" information available for 1KN2)

Asymmetric Unit(hide GO term definitions)

Chain L (Q58EU8_MOUSE | Q58EU8)

Asymmetric Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		PNE	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		ZN	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]
		AC6	[ RasMol ]	+environment [ RasMol ]
		AC7	[ RasMol ]	+environment [ RasMol ]
		AC8	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Glu H:148 - Pro H:149	[ RasMol ]
		Phe H:146 - Pro H:147	[ RasMol ]
		Phe L:94 - Pro L:95	[ RasMol ]
		Ser L:7 - Pro L:8	[ RasMol ]
		Trp H:197 - Pro H:198	[ RasMol ]
		Tyr L:140 - Pro L:141	[ RasMol ]

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]
		Biological Unit 3	[ Jena3D ]
		Biological Unit 4	[ Jena3D ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Asym. Unit - sites PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 1 - sites PNG format \| Biol. Unit 2 PNG format \| Biol. Unit 3 PNG format \| Biol. Unit 4 PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	1kn2
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	GCAA_MOUSE \| P01863
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt
	Q58EU8_MOUSE \| Q58EU8
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/TrEMBL

Access by Enzyme Classificator (EC Number)
	(no 'Enzyme Classificator' available)
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	GCAA_MOUSE \| P01863
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)
	Q58EU8_MOUSE \| Q58EU8
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

1kn4	CATALYTIC ANTIBODY D2.3 COMPLEX
1yec	STRUCTURE OF A CATALYTIC ANTIBODY IGG2A FAB FRAGMENT (D2.3)
1yef	STRUCTURE OF IGG2A FAB FRAGMENT (D2.3) COMPLEXED WITH SUBSTRATE ANALOGUE
1yeg	STRUCTURE OF IGG2A FAB FRAGMENT (D2.3) COMPLEXED WITH REACTION PRODUCT
1yeh	STRUCTURE OF IGG2A FAB FRAGMENT
1yei	CATALYTIC ANTIBODY D2.3 COMPLEX
1yej	CATALYTIC ANTIBODY COMPLEX
1yek	CATALYTIC ANTIBODY D2.3 COMPLEX

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 8)

Sites (8, 8)

SS Bonds (4, 4)

Cis Peptide Bonds (6, 6)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (4, 4)

CATH Domains (1, 4)

Pfam Domains (0, 0)

Gene Ontology (12, 12)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File