1H8O - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   THREE-DIMENSIONAL STRUCTURE OF ANTI-AMPICILLIN SINGLE CHAIN FV FRAGMENT.

Authors :   J. Burmester, S. Spinelli, L. Pugliese, A. Krebber, A. Honegger, S. Jun B. Schimmele, C. Cambillau, A. Pluckthun

Date :   14 Feb 01 (Deposition) - 02 Aug 01 (Release) - 29 Mar 17 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.75

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

Keywords :   Antibody, Fv Fragment, Anti-Ampicillin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Burmester, S. Spinelli, L. Pugliese, A. Krebber, A. Honegger, S. Jung, B. Schimmele, C. Cambillau, A. Pluckthun
Selection, Characterization And X-Ray Structure Of Anti-Ampicillin Single-Chain Fv Fragments From Phage-Displayed Murine Antibody Libraries
J. Mol. Biol. V. 309 671 2001
PubMed-ID: 11397088 | Reference-DOI: 10.1006/JMBI.2001.4663

Molecule 1 - MUTANT AL2 6E7P9G
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI K-12
	Expression System Plasmid	:	PAK3000
	Expression System Taxid	:	83333
	Expression System Variant	:	RV308
	Expression System Vector Type	:	PLASMID
	Fragment	:	FV FRAGMENT
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Other Details	:	SINGLE CHAIN FV ANTIBODY IN WHICH THE VL AND VH FRAGMENTS ARE JOINED BY A GGGGSGGGGSGGGGSGGGGS LINKER

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 2)

No.	Name	Count	Type	Full Name
1	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	SO4	-1	Ligand/Ion	SULFATE ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:11 , LYS A:12 , PHE A:13 , ARG B:111	BINDING SITE FOR RESIDUE SO4 A1000
2	AC2	SOFTWARE	LYS A:12 , ARG B:111	BINDING SITE FOR RESIDUE SO4 A1001

Asymmetric Unit

No.	Residues
1	A:26	-	A:91
2	A:153	-	A:227
3	B:26	-	B:91
4	B:153	-	B:227

Asymmetric Unit

No.	Residues
1	Tyr A:97	-	Pro A:98
2	Glu A:137	-	Pro A:138
3	Tyr B:97	-	Pro B:98
4	Glu B:137	-	Pro B:138

(no "SAP(SNP)/Variant" information available for 1H8O)

(no "PROSITE Motif" information available for 1H8O)

(no "Exon" information available for 1H8O)

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:220
                                                                                                                                                                                                                                                            
               SCOP domains d1h8oa1 A:4-111 Immunoglobulin light chain kappa variable domain, VL-kappa                                  d1h8oa2 A:132-243 Immunoglobulin heavy chain variable domain, VH                                                 SCOP domains
               CATH domains 1h8oA01 A:4-132 Immunoglobulins                                                                              1h8oA02 A:133-235 Immunoglobulins                                                                      -------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee...eeee.....eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhh.eeeeee......ee...eeeee..........eeee.....eeeeee....hhhhh.eeeeee.....eeeeeee......eee.hhhh....eeee....eeeeee...hhhhheeeeeee..ee...eeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1h8o A   4 DIVLTQSHKFMSTSVGDRVSITCKASQDVGTAVAWYQQKPGQSPKLLIYWASTRHTGVPDRFTGSGSGTDFTLTISNVQSEDLADYFCQQYSSYPLTFGAGTKLELKRQVQLQEPGGELVRPGASVKLSCKASGYTFTSYWINWVKQRPGQGLEWIGNIYPSDSYTNYNQKFKDKATLTVDKSSSTAYMQLSSLTSEDSAVYFCARWGYWGQGTLVTVSA 243
                                    13        23        33        43        53        63        73        83        93       103       133       143       153       163       173       183       193       203       213       223       233       243
                                                                                                                                     111|                                                                                                               
                                                                                                                                      132

Chain B from PDB  Type:PROTEIN  Length:220
                                                                                                                                                                                                                                                            
               SCOP domains d1h8ob1 B:4-112 Immunoglobulin light chain kappa variable domain, VL-kappa                                   d1h8ob2 B:133-243 Immunoglobulin heavy chain variable domain, VH                                                SCOP domains
               CATH domains 1h8oB01 B:4-111 Immunoglobulins                                                                             -1h8oB02 B:133-231 Immunoglobulins                                                                  ------------ CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee...eeee.....eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhh.eeeeee......ee...eeeee..........eeee.....eeeeee....hhhhh.eeeeee.....eeeeeee......eee.hhhh..eeeeeehhh.eeeeee...hhhhheeeeeee..ee...eeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1h8o B   4 DIVLTQSHKFMSTSVGDRVSITCKASQDVGTAVAWYQQKPGQSPKLLIYWASTRHTGVPDRFTGSGSGTDFTLTISNVQSEDLADYFCQQYSSYPLTFGAGTKLELKRGVQLQEPGGELVRPGASVKLSCKASGYTFTSYWINWVKQRPGQGLEWIGNIYPSDSYTNYNQKFKDKATLTVDKSSSTAYMQLSSLTSEDSAVYFCARWGYWGQGTLVTVSA 243
                                    13        23        33        43        53        63        73        83        93       103       133       143       153       163       173       183       193       203       213       223       233       243
                                                                                                                                      112|                                                                                                              
                                                                                                                                       133

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)

Mus musculus. Organism_taxid: 10090 (2)

1a	1h8oB01	B:4-111
1b	1h8oA01	A:4-132
1c	1h8oA02	A:133-235
1d	1h8oB02	B:133-231

(no "Pfam Domain" information available for 1H8O)

Asymmetric Unit(hide GO term definitions)

(no "Gene Ontology" information available for 1H8O)

Asymmetric Unit
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	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Glu A:137 - Pro A:138	[ RasMol ]
		Glu B:137 - Pro B:138	[ RasMol ]
		Tyr A:97 - Pro A:98	[ RasMol ]
		Tyr B:97 - Pro B:98	[ RasMol ]

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

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	1h8o
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1h8n	THREE-DIMENSIONAL STRUCTURE OF ANTI-AMPICILLIN SINGLE CHAIN FV FRAGMENT FROM PHAGE-DISPLAYED MURINE ANTIBODY LIBRARIES
1h8s	THREE-DIMENSIONAL STRUCTURE OF ANTI-AMPICILLIN SINGLE CHAIN FV FRAGMENT COMPLEXED WITH THE HAPTEN.

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (4, 4)

Cis Peptide Bonds (4, 4)

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SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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