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

Asym./Biol. Unit (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE SINGLE-CHAIN FV FRAGMENT 1696 IN COMPLEX WITH THE EPITOPE PEPTIDE CORRESPONDING TO N-TERMINUS OF HIV-2 PROTEASE

Authors :   P. Rezacova, J. Brynda, J. Lescar, G. A. Bentley, M. Fabry, M. Horejsi, J. Sedlacek

Date :   30 Mar 04 (Deposition) - 01 Mar 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.89

Chains :   Asym./Biol. Unit : A,B,C,D

Keywords :   Antibody-Antigen Complex; Hiv Inhibiting Antibody, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   P. Rezacova, J. Brynda, J. Lescar, M. Fabry, M. Horejsi, I. Sieglova, J. Sedlacek, G. A. Bentley
Crystal Structure Of A Cross-Reaction Complex Between An Anti-Hiv-1 Protease Antibody And An Hiv-2 Protease Peptide
J. Struct. Biol. V. 149 332 2005
PubMed-ID: 15721587 | Reference-DOI: 10.1016/J.JSB.2004.11.009
(for further references see the PDB file header)

Molecule 1 - SINGLE-CHAIN FV FRAGMENT 1696
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Strain	:	BL21 (DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	SCFV1696
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Other Details	:	T7 PROMOTER-DRIVEN PLASMID, INCLUSION BODIES PRODUCTION FOLLOWED BY PROTEIN IN VITRO REFOLDING
	Synonym	:	IGG1/KAPPA ANTIBODY; IMMUNOGLOBULIN

Molecule 2 - EPITOPE PEPTIDE CORRESPONDING TO N-TERMINUS OF HIV-2 PROTEASE
	Chains	:	C, D
	Engineered	:	YES
	Other Details	:	OCTAPEPTIDE PQFSLWKR
	Synthetic	:	YES

		1	2	3	4
Asymmetric/Biological Unit	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 1SVZ)

(no "Site" information available for 1SVZ)

Asymmetric/Biological Unit

No.	Residues
1	A:23	-	A:93
2	A:149	-	A:223
3	B:23	-	B:93
4	B:149	-	B:223

Asymmetric/Biological Unit

No.	Residues
1	Thr A:7	-	Pro A:8
2	Phe A:99	-	Pro A:100
3	Thr B:7	-	Pro B:8
4	Phe B:99	-	Pro B:100

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

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

(no "Exon" information available for 1SVZ)

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 A from PDB  Type:PROTEIN  Length:232
 aligned with KV2A7_MOUSE | P01631 from UniProtKB/Swiss-Prot  Length:113

    Alignment length:232
                                                                                                                                         112         113                                                                                                            
                                    10        20        30        40        50        60        70        80        90       100       110 |       -   |     -         -         -         -         -         -         -         -         -         -         -  
          KV2A7_MOUSE     1 DVVMTQTPLSLPVSLGDQASISCRSSQSLVHSNGNTYLNWYLQKAGQSPKLLIYKVSNRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGIYFCSQTTHVPPTFGGGTKLEIK-----------R------------------------------------------------------------------------------------------------------------   -
               SCOP domains d1svza1 A:1-112 Immunoglobulin light chain kappa variable domain, VL-kappa                                      d1svza2 A:128-247 Immunoglobulin heavy chain variable domain, VH                                                         SCOP domains
               CATH domains 1svzA01 A:1-128 Immunoglobulins                                                                                  1svzA02 A:129-227 Immunoglobulins                                                                  -------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee............eeeeee.....eeeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeee...eeee...eee.....eeeeeeee..hhhhh.eeeeee.....eeeeeee......eee.hhhh..eeeeeehhh.eeeeee...hhhhheeeeeeeeehhhheeeeee...eeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1svz A   1 DILMTQTPLYLPVSLGDQASISCRSSQTIVHNNGNTYLEWYLQKPGQSPQLLIYKVSNRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGIYYCFQGSHFPPTFGGGTKLEIKEVQLQQSGPELKKPGETVKISCKATNYAFTDYSMHWVKQAPGGDLKYVGWINTETDEPTFADDFKGRFAFSLDTSTSTAFLQINNLKNEDTATYFCVRDRHDYGEIFTYWGQGTTVTVSS 247
                                    10        20        30        40        50        60        70        80        90       100       110 ||    135       145       155       165       175       185       195       205       215       225       235       245  
                                                                                                                                         112|                                                                                                                       
                                                                                                                                          128

Chain B from PDB  Type:PROTEIN  Length:232
 aligned with KV2A7_MOUSE | P01631 from UniProtKB/Swiss-Prot  Length:113

    Alignment length:232
                                                                                                                                         112         113                                                                                                            
                                    10        20        30        40        50        60        70        80        90       100       110 |       -   |     -         -         -         -         -         -         -         -         -         -         -  
          KV2A7_MOUSE     1 DVVMTQTPLSLPVSLGDQASISCRSSQSLVHSNGNTYLNWYLQKAGQSPKLLIYKVSNRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGIYFCSQTTHVPPTFGGGTKLEIK-----------R------------------------------------------------------------------------------------------------------------   -
               SCOP domains d1svzb1 B:1-112 Immunoglobulin light chain kappa variable domain, VL-kappa                                      d1svzb2 B:128-247 Immunoglobulin heavy chain variable domain, VH                                                         SCOP domains
               CATH domains 1svzB01 B:1-128 Immunoglobulins                                                                                  1svzB02 B:129-227 Immunoglobulins                                                                  -------------------- CATH domains
           Pfam domains (1) ---V-set-1svzB01 B:4-111                                                                                       ------------------------------------------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) ---V-set-1svzB02 B:4-111                                                                                       ------------------------------------------------------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author ...eeee..eeee.....eeeeeee............eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeee...eeee...eee.....eeeeeeee........eeeeee.....eeeeeee......eee.hhhh..eeeeeehhh.eeeeee...hhhhh.eeeeeeeehhhheeeeee...eeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1svz B   1 DILMTQTPLYLPVSLGDQASISCRSSQTIVHNNGNTYLEWYLQKPGQSPQLLIYKVSNRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGIYYCFQGSHFPPTFGGGTKLEIKEVQLQQSGPELKKPGETVKISCKATNYAFTDYSMHWVKQAPGGDLKYVGWINTETDEPTFADDFKGRFAFSLDTSTSTAFLQINNLKNEDTATYFCVRDRHDYGEIFTYWGQGTTVTVSS 247
                                    10        20        30        40        50        60        70        80        90       100       110 ||    135       145       155       165       175       185       195       205       215       225       235       245  
                                                                                                                                         112|                                                                                                                       
                                                                                                                                          128

Chain C from PDB  Type:PROTEIN  Length:6
                                      
               SCOP domains ------ SCOP domains
               CATH domains ------ CATH domains
               Pfam domains ------ Pfam domains
         Sec.struct. author ...... Sec.struct. author
                 SAPs(SNPs) ------ SAPs(SNPs)
                    PROSITE ------ PROSITE
                 Transcript ------ Transcript
                 1svz C   1 PQFSLW   6

Chain D from PDB  Type:PROTEIN  Length:6
                                      
               SCOP domains ------ SCOP domains
               CATH domains ------ CATH domains
               Pfam domains ------ Pfam domains
         Sec.struct. author ...... Sec.struct. author
                 SAPs(SNPs) ------ SAPs(SNPs)
                    PROSITE ------ PROSITE
                 Transcript ------ Transcript
                 1svz D   1 PQFSLW   6

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	1svzA01	A:1-128
1b	1svzB01	B:1-128
1c	1svzA02	A:129-227
1d	1svzB02	B:129-227

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Ig (577)

Family: V-set (144)

Mus musculus (Mouse) (63)

1a	V-set-1svzB01	B:4-111
1b	V-set-1svzB02	B:4-111

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (KV2A7_MOUSE | P01631)

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.

Asymmetric/Biological Unit
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	Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 1svz)

	Sites
(no "Sites" information available for 1svz)

	Cis Peptide Bonds
		Phe A:99 - Pro A:100	[ RasMol ]
		Phe B:99 - Pro B:100	[ RasMol ]
		Thr A:7 - Pro A:8	[ RasMol ]
		Thr B:7 - Pro B:8	[ RasMol ]

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1cl2	FREE FAB 1696
1jp5	SCFV1696 IN COMPLEX WITH EPITOPE PEPTIDE CORRESPONDING TO N -TERMINUS OF HIV-1 PR
1mf2	FREE FAB F11 (ANTI-HIV PR ANTIBODY}
1n4x	FREE SCFV1696
2hrp	FAB F11 IN COMPLEX WITH THE EPITOPE PEPTIDE (HIV-1 PR RESIDUES 36-46)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (4, 4)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (2, 4)

CATH Domains (1, 4)

Pfam Domains (1, 2)

Gene Ontology (1, 1)

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