2VXU - JenaLib

Asymmetric Unit (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF MURINE REFERENCE ANTIBODY 125-2H FAB FRAGMENT

Authors :   M. A. Argiriadi, T. Xiang, C. Wu, T. Ghayur, D. W. Borhani

Date :   10 Jul 08 (Deposition) - 23 Jun 09 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.36

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

Keywords :   Fab, Il-18, Autoimmunity, Th1/Th2 Cells, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. A. Argiriadi, T. Xiang, C. Wu, T. Ghayur, D. W. Borhani
Unusual Water-Mediated Antigenic Recognition Of The Proinflammatory Cytokine Interleukin-18.
J. Biol. Chem. V. 284 24478 2009
PubMed-ID: 19553661 | Reference-DOI: 10.1074/JBC.M109.023887

Molecule 1 - MURINE IGG 125-2H
	Cell Line	:	HYBRIDOMA
	Chains	:	H, I
	Engineered	:	YES
	Expression System	:	MUS MUSCULUS
	Expression System Taxid	:	10090
	Organism Common	:	MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090

Molecule 2 - MURINE IGG 125-2H
	Cell Line	:	HYBRIDOMA
	Chains	:	L, M
	Engineered	:	YES
	Expression System	:	MUS MUSCULUS
	Expression System Taxid	:	10090
	Organism Common	:	MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090

		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)

(no "Ligand,Modified Residues,Ions" information available for 2VXU)

(no "Site" information available for 2VXU)

Asymmetric Unit

No.	Residues
1	H:22	-	H:92
2	H:140	-	H:195
3	H:215	-	L:214
4	I:22	-	I:92
5	I:140	-	I:195
6	I:215	-	M:214
7	L:23	-	L:88
8	L:134	-	L:194
9	M:23	-	M:88
10	M:134	-	M:194

Asymmetric Unit

No.	Residues
1	Phe H:146	-	Pro H:147
2	Glu H:148	-	Pro H:149
3	Trp H:188	-	Pro H:189
4	Phe I:146	-	Pro I:147
5	Glu I:148	-	Pro I:149
6	Trp I:188	-	Pro I:189
7	Ser L:7	-	Pro L:8
8	Ser L:94	-	Pro L:95
9	Tyr L:140	-	Pro L:141
10	Ser M:7	-	Pro M:8
11	Ser M:94	-	Pro M:95
12	Tyr M:140	-	Pro M:141

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

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

(no "Exon" information available for 2VXU)

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:216
                                                                                                                                                                                                                                                        
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 2vxuH01 H:1-113 Immunoglobulins                                                                                  2vxuH02 H:114-212 Immunoglobulins                                                                  ---- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee..hhhhh.eeeeeee...eeeeeeee......eee.......eeeeee....eeeeee...hhhhheeeeeee...ee...eeeee........eeeee..........eeeeeeeeeee.....eeee.hhh....eee...eee..eeeeeeeeeee.........eeeeeehhhheeeeee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2vxu H   1 EIQLQQSGPELVKPGASVKVSCKASGYSFTDYFIYWVKQSHGKSLEWIGDIDPYNGDTSYNQKFRDKATLTVDQSSTTAFMHLNSLTSEDSAVYFCARGLRFWGQGTLVTVSAAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPRDCG 216
                                    10        20        30        40        50  |     59        69        79   |||  86        96|      110       120       130       140       150       160       170       180       190       200       210      
                                                                              52A                            82A||            96|                                                                                                                   
                                                                                                              82B|            101                                                                                                                   
                                                                                                               82C

Chain I from PDB  Type:PROTEIN  Length:216
                                                                                                                                                                                                                                                        
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 2vxuI01 I:1-113 Immunoglobulins                                                                                  2vxuI02 I:114-212 Immunoglobulins                                                                  ---- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee..hhhhh.eeeeeee...eeeeeeee......eee.......eeeeee....eeeeee...hhhhheeeeeee...ee...eeeee........eeeee..........eeeeeeeeeee.....eeee.hhh....eee...eee..eeeeeeeeeee.........eeeeeehhhheeeeee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2vxu I   1 EIQLQQSGPELVKPGASVKVSCKASGYSFTDYFIYWVKQSHGKSLEWIGDIDPYNGDTSYNQKFRDKATLTVDQSSTTAFMHLNSLTSEDSAVYFCARGLRFWGQGTLVTVSAAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPRDCG 216
                                    10        20        30        40        50  |     59        69        79   |||  86        96|      110       120       130       140       150       160       170       180       190       200       210      
                                                                              52A                            82A||            96|                                                                                                                   
                                                                                                              82B|            101                                                                                                                   
                                                                                                               82C

Chain L from PDB  Type:PROTEIN  Length:214
                                                                                                                                                                                                                                                      
               SCOP domains d2vxul1 L:1-107 automated matches                                                                          d2vxul2 L:108-214 automated matches                                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------2vxuL02 L:109-211 Immunoglobulins                                                                      --- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee.......eeeeee.....eeeeee...ee.......eeeeee..eeeeee...hhhhh.eeeeee......ee...eeeee.......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhh...eeeeeee.......eeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vxu L   1 DIQMTQSPSSLSASLGERVSLTCRASQDIGSKLYWLQQEPDGTFKRLIYATSSLDSGVPKRFSGSRSGSDYSLTISSLESEDFVDYYCLQYASSPYTFGGGTKLAIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC 214
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210

Chain M from PDB  Type:PROTEIN  Length:214
                                                                                                                                                                                                                                                      
               SCOP domains d2vxum1 M:1-107 automated matches                                                                          d2vxum2 M:108-214 automated matches                                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------2vxuM02 M:109-211 Immunoglobulins                                                                      --- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee.......eeeeee.....eeeeee...ee.......eeeeee..eeeeee...hhhhh.eeeeee......ee...eeeee.......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhh...eeeeeee.......eeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vxu M   1 DIQMTQSPSSLSASLGERVSLTCRASQDIGSKLYWLQQEPDGTFKRLIYATSSLDSGVPKRFSGSRSGSDYSLTISSLESEDFVDYYCLQYASSPYTFGGGTKLAIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC 214
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210

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(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: Immunoglobulin-like beta-sandwich (7299)

Superfamily: Immunoglobulin (5995)

Family: automated matches (864)

Protein domain: automated matches (864)

Mouse (Mus musculus) [TaxId: 10090] (360)

1a	d2vxul1	L:1-107
1b	d2vxum1	M:1-107

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

Protein domain: automated matches (652)

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

2a	d2vxul2	L:108-214
2b	d2vxum2	M:108-214

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Immunoglobulin-like (3897)

Homologous Superfamily: Immunoglobulins (2282)

Mouse (Mus musculus) (152)

1a	2vxuL02	L:109-211
1b	2vxuM02	M:109-211
1c	2vxuH02	H:114-212
1d	2vxuI02	I:114-212
1e	2vxuH01	H:1-113
1f	2vxuI01	I:1-113

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

Asymmetric Unit(hide GO term definitions)

(no "Gene Ontology" information available for 2VXU)

Asymmetric Unit
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	Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 2vxu)

	Sites
(no "Sites" information available for 2vxu)

	Cis Peptide Bonds
		Glu H:148 - Pro H:149	[ RasMol ]
		Glu I:148 - Pro I:149	[ RasMol ]
		Phe H:146 - Pro H:147	[ RasMol ]
		Phe I:146 - Pro I:147	[ RasMol ]
		Ser L:7 - Pro L:8	[ RasMol ]
		Ser L:94 - Pro L:95	[ RasMol ]
		Ser M:7 - Pro M:8	[ RasMol ]
		Ser M:94 - Pro M:95	[ RasMol ]
		Trp H:188 - Pro H:189	[ RasMol ]
		Trp I:188 - Pro I:189	[ RasMol ]
		Tyr L:140 - Pro L:141	[ RasMol ]
		Tyr M:140 - Pro M:141	[ RasMol ]

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

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	2vxu
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2vxt	CRYSTAL STRUCTURE OF HUMAN IL-18 COMPLEXED TO MURINE REFERENCE ANTIBODY 125-2H FAB
2vxv	CRYSTAL STRUCTURE OF HUMAN IGG ABT-325 FAB FRAGMENT

Description

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Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (10, 10)

Cis Peptide Bonds (12, 12)

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SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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SCOP Domains (2, 4)

CATH Domains (1, 6)

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