1P4B - JenaLib

Title :   THREE-DIMENSIONAL STRUCTURE OF A SINGLE CHAIN FV FRAGMENT COMPLEXED WITH THE PEPTIDE GCN4(7P-14P).

Authors :   C. Zahnd, S. Spinelli, B. Luginbuhl, L. Jermutus, P. Amstutz, C. Cambillau, A. Pluckthun

Date :   22 Apr 03 (Deposition) - 04 May 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.35

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

Keywords :   Fv Antibody, Antigen Peptide Binder, Scfv, Picomolar Binder, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. Zahnd, S. Spinelli, P. Amstutz, C. Cambillau
Directed In Vitro Evolution And Crystallographic Analysis Of A Peptide-Binding Single Chain Antibody Fragment (Scfv) With Low Picomolar Affinity.
J. Biol. Chem. V. 279 18870 2004
PubMed-ID: 14754898 | Reference-DOI: 10.1074/JBC.M309169200
(for further references see the PDB file header)

Compounds

Molecule 1 - ANTIBODY VARIABLE LIGHT CHAIN
	Chains	:	L
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PAK400
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Synonym	:	IG LAMBDA-1 CHAIN V REGION S43

Molecule 2 - ANTIBODY VARIABLE HEAVY CHAIN
	Chains	:	H
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PAK400
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090

Molecule 3 - GCN4(7P-14P) PEPTIDE
	Chains	:	P
	Engineered	:	YES
	Other Details	:	THE PEPTIDE WAS CHEMICALLY SYNTHESIZED.
	Synthetic	:	YES

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (2, 2)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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
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Chain H from PDB  Type:PROTEIN  Length:112
 aligned with HVM44_MOUSE | P01820 from UniProtKB/Swiss-Prot  Length:115

    Alignment length:112
                                                                                                                         115                
                                    29        39        49        59        69        79        89        99       109     |   -         -  
          HVM44_MOUSE    20 QVQLKESGPGLVAPSQSLSITCTVSGFSLTGYGVNWVRQPPGKGLEWLGMIWGDGSTDYNSALKSRLSISKDNSKSQVFLKMNSLQTDDTARYYCA----------------   -
               SCOP domains d1p4bh_ H: Immunoglobulin heavy chain variable domain, VH                                                        SCOP domains
               CATH domains 1p4bH00 H:1-148 Immunoglobulins                                                                                  CATH domains
               Pfam domains ------V-set-1p4bH01 H:7-106                                                                    ----------------- Pfam domains
         Sec.struct. author ..eeeeeeee.......eeeeeeee........eeeeee.....eeeeeee.....eee...hhh.eeeeee....eeeeee...hhhhheeeeee..........eee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------- Transcript
                 1p4b H   1 DVQLQQSGPGLVAPSQSLSITCTVSGFSLTDYGVNWVRQSPGKGLEWLGVIWGDGITDYNSALKSRLSVTKDNSKSQVFLKMNSLQSGDSARYYCVTGLFDYWGQGTTLTVS 148
                                  ||11        21     || 32||      47        57  ||    71        81        91       101       136       146  
                                  7|                27|  33|                   60|                                          110|            
                                   9                 29   39                    65                                           136

Chain L from PDB  Type:PROTEIN  Length:110
 aligned with LV1A_MOUSE | P01723 from UniProtKB/Swiss-Prot  Length:117

    Alignment length:110
                                                                                                                           117            
                                    29        39        49        59        69        79        89        99       109       | -         -
           LV1A_MOUSE    20 SQAVVTQESALTTSPGETVTLTCRSSTGAVTTSNYANWVQEKPDHLFTGLIGGTNNRAPGVPARFSGSLIGDKAALTITGAQTEDEAIYFCALWYSNH------------   -
               SCOP domains d1p4bl_ L: Immunoglobulin light chain lambda variable domain, VL-lambda                                        SCOP domains
               CATH domains 1p4bL00 L:0-148 Immunoglobulins                                                                                CATH domains
               Pfam domains --V-set-1p4bL01 L:2-136                                                                           ------------ Pfam domains
         Sec.struct. author ....ee...eeee....eeeeeeee.....hhhhh.eeeeeehhheeeeeee...ee.......eeeeee..eeeeeee..hhhhheeeeeeee....eee...eeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------- Transcript
                 1p4b L   0 ADAVVTQESALTTSPGETVTLTCRSSTGAVTTSNYASWVQEKPDHLFTGLIGGTNNRAPGVPARFSGSLIGDKAALTITGAQTEDEAIYFCALWYSNHWVFGGGTKLTVL 148
                                   |10        20      ||31 ||     45        55  ||    73        83||      95       105     ||138       148
                                   7|                27|  33|                  58|               84|                     111|             
                                    9                 29   38                   67                87                      135

Chain P from PDB  Type:PROTEIN  Length:12
                                            
               SCOP domains ------------ SCOP domains
               CATH domains ------------ CATH domains
               Pfam domains ------------ Pfam domains
         Sec.struct. author hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------ SAPs(SNPs)
                    PROSITE ------------ PROSITE
                 Transcript ------------ Transcript
                 1p4b P   1 AHLENEVARLKK  12
                                    10

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 '\|'

Classification and Annotation

SCOP Domains (2, 2)

CATH Domains (1, 2)

Pfam Domains (1, 2)

Gene Ontology (2, 3)

Asymmetric/Biological Unit(hide GO term definitions)

Chain H (HVM44_MOUSE | P01820)

molecular function
	GO:0003823		antigen binding		Interacting selectively and non-covalently with an antigen, any substance which is capable of inducing a specific immune response and of reacting with the products of that response, the specific antibody or specifically sensitized T-lymphocytes, or both. Binding may counteract the biological activity of the antigen.

Chain L (LV1A_MOUSE | P01723)

molecular function
	GO:0003823	antigen binding	Interacting selectively and non-covalently with an antigen, any substance which is capable of inducing a specific immune response and of reacting with the products of that response, the specific antibody or specifically sensitized T-lymphocytes, or both. Binding may counteract the biological activity of the antigen.
cellular component
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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