1N4X - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   STRUCTURE OF SCFV 1696 AT ACIDIC PH

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

Date :   02 Nov 02 (Deposition) - 10 Jun 03 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.70

Chains :   Asym. Unit : H,I,L,M
Biol. Unit 1: H,L  (1x)
Biol. Unit 2: I,M  (1x)

Keywords :   Immunoglobulin, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Lescar, J. Brynda, M. Fabry, M. Horejsi, P. Rezacova, J. Sedlacek, G. A. Bentley
Structure Of A Single-Chain Fv Fragment Of An Antibody That Inhibits The Hiv-1 And Hiv-2 Proteases.
Acta Crystallogr. , Sect. D V. 59 955 2003
PubMed-ID: 12777823 | Reference-DOI: 10.1107/S0907444903003597
(for further references see the PDB file header)

Molecule 1 - IMMUNOGLOBULIN KAPPA CHAIN VARIABLE REGION
	Chains	:	L, M
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Synonym	:	SCFV 1696 MOLECULE 1, MONOCLONAL ANTIBODY 1696

Molecule 2 - IMMUNOGLOBULIN HEAVY CHAIN VARIABLE REGION
	Chains	:	H, I
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Synonym	:	SCFV 1696 MOLECULE 2, MONOCLONAL ANTIBODY 1696

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 2)

No.	Name	Count	Type	Full Name
1	CL	2	Ligand/Ion	CHLORIDE ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP I:399 , ARG I:400 , HIS I:401 , TYR I:403 , GLY I:404 , GLU I:405 , ILE I:406 , HOH I:1073	BINDING SITE FOR RESIDUE CL I 1001
2	AC2	SOFTWARE	ASP H:399 , ARG H:400 , HIS H:401 , TYR H:403 , GLY H:404 , GLU H:405 , ILE H:406	BINDING SITE FOR RESIDUE CL H 1002

Asymmetric Unit

No.	Residues
1	H:322	-	H:396
2	I:322	-	I:396
3	L:23	-	L:93
4	M:23	-	M:93

Asymmetric Unit

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

(no "SAP(SNP)/Variant" information available for 1N4X)

(no "PROSITE Motif" information available for 1N4X)

(no "Exon" information available for 1N4X)

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:120
 aligned with Q921A6_MOUSE | Q921A6 from UniProtKB/TrEMBL  Length:241

    Alignment length:120
                                                                                                                            98 99                   
                                    10        20        30        40        50        60        70        80        90       | -|      108       118
         Q921A6_MOUSE     1 QVKLQQSGPELKKPGETVKISCKASGYTFTDYGMNWVKQAPGKGLKWMGWINTYTGEPTYADDFKGRFAFSLETSASTAYLQINNLKNEDTATYFCAR--KDLLRYFDYWGQGTTVTVSS 118
               SCOP domains d1n4xh_ H: Immunoglobulin heavy chain variable domain, VH                                                                SCOP domains
               CATH domains 1n4xH00 H:301-420 Immunoglobulins                                                                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee..hhhhh.eeeeee.....eeeeeeee....eeee.......eeeeeehhh.eeeeee...hhhhheeeeeeee.......eeee...eeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------ Transcript
                 1n4x H 301 EVQLQQSGPELKKPGETVKISCKATNYAFTDYSMHWVKQAPGGDLKYVGWINTETDEPTFADDFKGRFAFSLDTSTSTAFLQINNLKNEDTATYFCVRDRHDYGEIFTYWGQGTTVTVSA 420
                                   310       320       330       340       350       360       370       380       390       400       410       420

Chain I from PDB  Type:PROTEIN  Length:119
 aligned with Q921A6_MOUSE | Q921A6 from UniProtKB/TrEMBL  Length:241

    Alignment length:119
                                                                                                                            98 99                  
                                    10        20        30        40        50        60        70        80        90       | -|      108         
         Q921A6_MOUSE     1 QVKLQQSGPELKKPGETVKISCKASGYTFTDYGMNWVKQAPGKGLKWMGWINTYTGEPTYADDFKGRFAFSLETSASTAYLQINNLKNEDTATYFCAR--KDLLRYFDYWGQGTTVTVS 117
               SCOP domains d1n4xi_ I: Immunoglobulin heavy chain variable domain, VH                                                               SCOP domains
               CATH domains 1n4xI00 I:301-419 Immunoglobulins                                                                                       CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee..hhhhh.eeeeee.....eeeeeee......eee.hhhh..eeeeeehhh.eeeeee...hhhhheeeeeeee.......eeee...eeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------- Transcript
                 1n4x I 301 EVQLQQSGPELKKPGETVKISCKATNYAFTDYSMHWVKQAPGGDLKYVGWINTETDEPTFADDFKGRFAFSLDTSTSTAFLQINNLKNEDTATYFCVRDRHDYGEIFTYWGQGTTVTVS 419
                                   310       320       330       340       350       360       370       380       390       400       410

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

    Alignment length:113
                             1                                                                                                               
                             |       9        19        29        39        49        59        69        79        89        99       109   
          KV2A7_MOUSE     - -DVVMTQTPLSLPVSLGDQASISCRSSQSLVHSNGNTYLNWYLQKAGQSPKLLIYKVSNRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGIYFCSQTTHVPPTFGGGTKLEIK 112
               SCOP domains d1n4xl_ L: Immunoglobulin light chain kappa variable domain, VL-kappa                                             SCOP domains
               CATH domains 1n4xL00 L:0-112 Immunoglobulins                                                                                   CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee..eeee.....eeeeeee............eeeeee......eeeee...ee.......eeeee...eeeeee...hhhhheeeeeee......ee...eeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------- Transcript
                 1n4x L   0 MDILMTQTPLYLPVSLGDQASISCRSSQTIVHNNGNTYLEWYLQKPGQSPQLLIYKVSNRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGIYYCFQGSHFPPTFGGGTKLEIA 112
                                     9        19        29        39        49        59        69        79        89        99       109

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

    Alignment length:113
                             1                                                                                                               
                             |       9        19        29        39        49        59        69        79        89        99       109   
          KV2A7_MOUSE     - -DVVMTQTPLSLPVSLGDQASISCRSSQSLVHSNGNTYLNWYLQKAGQSPKLLIYKVSNRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGIYFCSQTTHVPPTFGGGTKLEIK 112
               SCOP domains d1n4xm_ M: Immunoglobulin light chain kappa variable domain, VL-kappa                                             SCOP domains
               CATH domains 1n4xM00 M:0-112 Immunoglobulins                                                                                   CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee..eeee.....eeeeeee............eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------- Transcript
                 1n4x M   0 MDILMTQTPLYLPVSLGDQASISCRSSQTIVHNNGNTYLEWYLQKPGQSPQLLIYKVSNRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGIYYCFQGSHFPPTFGGGTKLEIA 112
                                     9        19        29        39        49        59        69        79        89        99       109

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	1n4xL00	L:0-112
1b	1n4xM00	M:0-112
1c	1n4xI00	I:301-419
1d	1n4xH00	H:301-420

(no "Pfam Domain" information available for 1N4X)

Asymmetric Unit(hide GO term definitions)

Chain H,I (Q921A6_MOUSE | Q921A6)

Chain L,M (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.

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	Cis Peptide Bonds
		Phe L:99 - Pro L:100	[ RasMol ]
		Phe M:99 - Pro M:100	[ RasMol ]
		Thr L:7 - Pro L:8	[ RasMol ]
		Thr M:7 - Pro M:8	[ RasMol ]

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	Q921A6_MOUSE \| Q921A6
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UniProtKB/Swiss-Prot
	KV2A7_MOUSE \| P01631	:	1bfv 1cfv 1dlf 1maj 1mak 1svz 1wz1 2bfv 2dlf 2hkf 2hkh 2ipt 2iqa 2o5x 2o5y 2o5z 2r0w 2vq1
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	Q921A6_MOUSE \| Q921A6	:	1zea

1cl7	FREE FAB 1696
1jp5	COMPLEXED SCFV1696

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (4, 4)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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SCOP Domains (2, 4)

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