1KEL - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CATALYTIC ANTIBODY 28B4 FAB FRAGMENT COMPLEXED WITH HAPTEN (1-[N-4'-NITROBENZYL-N-4'-CARBOXYBUTYLAMINO] METHYLPHOSPHONIC ACID)

Authors :   L. C. Hsieh-Wilson, P. G. Schultz, R. C. Stevens

Date :   16 Apr 96 (Deposition) - 07 Dec 96 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

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

Keywords :   Sulfide Oxidation, Monooxygenase, Oxygenation, Fab, Immunoglobulin, Catalytic Antibody (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   L. C. Hsieh-Wilson, P. G. Schultz, R. C. Stevens
Insights Into Antibody Catalysis: Structure Of An Oxygenation Catalyst At 1. 9-Angstrom Resolution.
Proc. Natl. Acad. Sci. Usa V. 93 5363 1996
PubMed-ID: 8643580 | Reference-DOI: 10.1073/PNAS.93.11.5363
(for further references see the PDB file header)

Molecule 1 - 28B4 FAB
	Cell Line	:	28B4
	Chains	:	L
	Fragment	:	VARIABLE REGIONS OF LIGHT AND HEAVY CHAINS
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Other Details	:	THIS PROTEIN IS A FAB FRAGMENT PRODUCED UPON THE DIGESTION OF FULL-LENGTH MURINE MONOCLONAL ANTIBODY BY PAPAIN
	Strain	:	BALB/C

Molecule 2 - 28B4 FAB
	Cell Line	:	28B4
	Chains	:	H
	Fragment	:	VARIABLE REGIONS OF LIGHT AND HEAVY CHAINS
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Other Details	:	THIS PROTEIN IS A FAB FRAGMENT PRODUCED UPON THE DIGESTION OF FULL-LENGTH MURINE MONOCLONAL ANTIBODY BY PAPAIN
	Strain	:	BALB/C

		1	2
Asymmetric/Biological Unit	:	H	L

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 1)

No.	Name	Count	Type	Full Name
1	AAH	1	Ligand/Ion	1-[N-4'-NITROBENZYL-N-4'-CARBOXYBUTYLAMINO]METHYLPHOSPHONIC ACID

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TYR H:33 , ASN H:35 , PHE H:50 , ARG H:52 , LYS H:56 , TRP H:101 , TYR L:37 , PHE L:94 , GLY L:96	BINDING SITE FOR RESIDUE AAH H 219

Asymmetric/Biological Unit

No.	Residues
1	H:22	-	H:98
2	H:146	-	H:201
3	L:23	-	L:93
4	L:139	-	L:199

Asymmetric/Biological Unit

No.	Residues
1	Thr L:7	-	Pro L:8
2	Val L:99	-	Pro L:100
3	Tyr L:145	-	Pro L:146
4	Phe H:152	-	Pro H:153
5	Glu H:154	-	Pro H:155
6	Arg H:194	-	Pro H:195

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

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

(no "Exon" information available for 1KEL)

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:218
                                                                                                                                                                                                                                                          
               SCOP domains d1kelh1 H:1-115 Immunoglobulin heavy chain variable domain, VH                                                     d1kelh2 H:116-218 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                         SCOP domains
               CATH domains 1kelH01 H:1-119 Immunoglobulins                                                                                        1kelH02 H:120-218 Immunoglobulins                                                                   CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..eee.....eeeeeeee...hhh.eeeeeee.....eeeeeee........eee.......eeeeee....eeeeee....hhh.eeeeeeee...........eeeee........eeeee..........eeeeeeeeeee.....eeee........eee...eee..eeeeeeeeeeehhh......eeeeeehhh.eeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1kel H   1 EVKLVESGGGLGQPGGSLRLSCATSGFTFTDYYFNWARQPPGKALEWLGFIRNKAKGYTTEYSASVKGRFTISRDNSQGILYLQMNTLRAEDSATYYCARWGSYAMDYWGQGTSVTVSSAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSPRPSETVTCNVAHPASSTKVDKKIVP 218
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210

Chain L from PDB  Type:PROTEIN  Length:217
                                                                                                                                                                                                                                                         
               SCOP domains d1kell1 L:1-112 Immunoglobulin light chain kappa variable domain, VL-kappa                                      d1kell2 L:113-217 Immunoglobulin light chain kappa constant domain, CL-kappa                              SCOP domains
               CATH domains 1kelL01 L:1-113 Immunoglobulins                                                                                  1kelL02 L:114-216 Immunoglobulins                                                                      - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee.............eeeee......eeee.............eeeeee..eeeeee....hhh..eeeee.............eeee.......eeeee...hhhhhh.eeeeeeeee.......eeeeee........eeeee...........eeeeeeeehhhhhh..eeeeeee.......eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1kel L   1 DVLMTQTPLSLPVSLGDQASISCRFSQSIVHSNGNTYLEWYLQKSGQSPKLLIYKVSNRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGVYYCFQGSHVPRTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRN 217
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210

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/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	1kelL02	L:114-216
1b	1kelL01	L:1-113
1c	1kelH02	H:120-218
1d	1kelH01	H:1-119

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

Asymmetric/Biological Unit(hide GO term definitions)

Asymmetric/Biological 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
		AAH	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Arg H:194 - Pro H:195	[ RasMol ]
		Glu H:154 - Pro H:155	[ RasMol ]
		Phe H:152 - Pro H:153	[ RasMol ]
		Thr L:7 - Pro L:8	[ RasMol ]
		Tyr L:145 - Pro L:146	[ RasMol ]
		Val L:99 - Pro L:100	[ RasMol ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym./Biol. Unit PNG format \| Asym./Biol. Unit - sites 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
	1kel
		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
	IGHG1_MOUSE \| P01868
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

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
	IGHG1_MOUSE \| P01868
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

(no "Related Entries Specified in the PDB File" available for 1KEL)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 1)

Sites (1, 1)

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 (17, 17)

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