2IQ9 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   PFA2 FAB FRAGMENT, TRICLINIC APO FORM

Authors :   A. S. Gardberg, C. Dealwis

Date :   13 Oct 06 (Deposition) - 09 Oct 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

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

Keywords :   Pfa2, Wwddd, Cdr, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. S. Gardberg, L. T. Dice, S. Ou, R. L. Rich, E. Helmbrecht, J. Ko, R. Wetzel, D. G. Myszka, P. H. Patterson, C. Dealwis
Molecular Basis For Passive Immunotherapy Of Alzheimer'S Disease
Proc. Natl. Acad. Sci. Usa V. 104 15659 2007
PubMed-ID: 17895381 | Reference-DOI: 10.1073/PNAS.0705888104

Molecule 1 - IGG2A FAB FRAGMENT PFA2 KAPPA LIGHT CHAIN
	Chains	:	L
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Other Details	:	HYBRIDOMA
	Strain	:	BALB/C

Molecule 2 - IGG2A FAB FRAGMENT PFA2 HEAVY CHAIN
	Chains	:	H
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Other Details	:	HYBRIDOMA
	Strain	:	BALB/C

		1	2
Asymmetric/Biological Unit	:	H	L

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 2)

No.	Name	Count	Type	Full Name
1	ACM	2	Ligand/Ion	ACETAMIDE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	VAL H:127 , CYS H:128 , ARG H:213 , PRO L:118 , ASN L:209 , CYS L:213	BINDING SITE FOR RESIDUE ACM L 1219
2	AC2	SOFTWARE	CYS H:128 , ARG H:213 , ASP L:60 , GLU L:212 , CYS L:213	BINDING SITE FOR RESIDUE ACM H 1138

Asymmetric/Biological Unit

No.	Residues
1	H:22	-	H:92
2	H:140	-	H:195
3	L:23	-	L:88
4	L:133	-	L:193

Asymmetric/Biological Unit

No.	Residues
1	Thr L:7	-	Pro L:8
2	Val L:94	-	Pro L:95
3	Tyr L:139	-	Pro L:140
4	Phe H:146	-	Pro H:147
5	Glu H:148	-	Pro H:149
6	Ser H:172	-	Gly H:173
7	Trp H:188	-	Pro H:189

(no "SAP(SNP)/Variant" information available for 2IQ9)

(no "PROSITE Motif" information available for 2IQ9)

(no "Exon" information available for 2IQ9)

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:221
                                                                                                                                                                                                                                                              
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2iq9H01 H:1-113 Immunoglobulins                                                                                            2iq9H02 H:114-212 Immunoglobulins                                                                - CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee.....................................hhhh.....................hhhhh..................................eeeee............................................................................hhhh.......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2iq9 H    1 QVTLKESGPGILKPSQTLSLTCSLSGFSLRTSGMGVGWIRQPSGKGLEWLAHIWWDDDKNYNPSLKSQLTISKDTSRNQVFLKITSVDTADTATYYCVRRAHNVVLGDWFAYWGQGTLVTVSAAKTTAPSVYPLAPVCTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSGLYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEPR  213
                                    10        20        30     || 38        48        58        68        78    ||| 85        95     |100E       110       120       132       142       152       162       172       182       192       202       212 
                                                             35A|                                             82A||               100A||||                         128|                                                                                  
                                                              35B                                              82B|                100B|||                          131                                                                                  
                                                                                                                82C                 100C||                                                                                                               
                                                                                                                                     100D|                                                                                                               
                                                                                                                                      100E

Chain L from PDB  Type:PROTEIN  Length:219
 aligned with A2NHM3_MOUSE | A2NHM3 from UniProtKB/TrEMBL  Length:219

    Alignment length:219
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210         
        A2NHM3_MOUSE      1 DVLMTQTPLSLPVSLGDQASISCRSSQSIVHTNGNTYLEWYLQKPGQSPKLLIYKVSNRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGVYYCFQGSHVPRTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC  219
               SCOP domains d2iq9l1 L:1-106A automated matches                                                                              d2iq9l2 L:107-213 automated matches                                                                         SCOP domains
               CATH domains 2iq9L01 L:1-107 Immunoglobulins                                                                                  -2iq9L02 L:109-208 Immunoglobulins                                                                   ----- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee..........................................................hhhhh.....................................hhhhhh........................................................hhhhhhh......................hhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2iq9 L    1 DVLMTQTPLSLPVSLGDQASISCRSSQSIVHSNGNTYLEWYLQKPGQSPKLLIYKVSNRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGVYYCFQGSHVPLTFGAGTKLELKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC  213
                                    10        20       27C||      35        45        55        65        75        85        95       105 |     114       124       134       144       154       164       174       184       194       204         
                                                     27A||||                                                                            106A                                                                                                           
                                                      27B|||                                                                                                                                                                                           
                                                       27C||                                                                                                                                                                                           
                                                        27D|                                                                                                                                                                                           
                                                         27E

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(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: Immunoglobulin-like beta-sandwich (7299)

Superfamily: Immunoglobulin (5995)

Family: C1 set domains (antibody constant domain-like) (3013)

Protein domain: automated matches (652)

Mouse (Mus musculus) [TaxId: 10090] (309)

d2iq9l2

L:107-213

Family: V set domains (antibody variable domain-like) (1919)

Protein domain: automated matches (311)

Mouse (Mus musculus) [TaxId: 10090] (112)

d2iq9l1

L:1-106A

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	2iq9L02	L:109-208
1b	2iq9L01	L:1-107
1c	2iq9H02	H:114-212
1d	2iq9H01	H:1-113

(no "Pfam Domain" information available for 2IQ9)

Asymmetric/Biological Unit(hide GO term definitions)

Chain L (A2NHM3_MOUSE | A2NHM3)

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Glu H:148 - Pro H:149	[ RasMol ]
		Phe H:146 - Pro H:147	[ RasMol ]
		Ser H:172 - Gly H:173	[ RasMol ]
		Thr L:7 - Pro L:8	[ RasMol ]
		Trp H:188 - Pro H:189	[ RasMol ]
		Tyr L:139 - Pro L:140	[ RasMol ]
		Val L:94 - Pro L:95	[ RasMol ]

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	2iq9
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		Orientation in Membranes	:	OPM
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2ipt	PFA1 FAB FRAGMENT
2ipu	PFA1 FAB FRAGMENT COMPLEXED WITH ABETA 1-8 PEPTIDE
2iqa	PFA2 FAB FRAGMENT, MONOCLINIC APO FORM
2iqb	PFA2 FAB FRAGMENT BOUND TO ABETA 1-8

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (4, 4)

Cis Peptide Bonds (7, 7)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (2, 2)

CATH Domains (1, 4)

Pfam Domains (0, 0)

Gene Ontology (2, 2)

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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File