1T04 - JenaLib

Asymmetric Unit (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   THREE DIMENSIONAL STRUCTURE OF A HUMANIZED ANTI-IFN-GAMMA FAB IN C2 SPACE GROUP

Authors :   P. C. Bourne, S. S. Terzyan, G. Cloud, N. F. Landolfi, M. Vasquez, A. B. Edmundson

Date :   07 Apr 04 (Deposition) - 05 Oct 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.00

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: C,D  (1x)

Keywords :   Antibody Engineering, Humanized And Chimeric Antibody, Fab, X-Ray Structure, Three-Dimensional Structure, Gamma- Interferon, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   P. C. Bourne, S. S. Terzyan, G. Cloud, N. F. Landolfi, M. Vasquez, A. B. Edmundson
Three-Dimensional Structures Of A Humanized Anti-Ifn-Gamma Fab (Huzaf) In Two Crystal Forms.
Acta Crystallogr. , Sect. D V. 60 1761 2004
PubMed-ID: 15388922 | Reference-DOI: 10.1107/S0907444904018670
(for further references see the PDB file header)

Molecule 1 - HUZAF ANTIBODY LIGHT CHAIN
	Chains	:	A, C
	Engineered	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Other Details	:	THE SOURCE IS ENGINEERED HUMAN CONSTANT AND FRAMEWORK REGIONS WITH CDRS FROM MOUSE.
	Synonym	:	FAB

Molecule 2 - HUZAF ANTIBODY HEAVY CHAIN
	Chains	:	B, D
	Engineered	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Other Details	:	THE SOURCE IS ENGINEERED HUMAN CONSTANT AND FRAMEWORK REGIONS WITH CDRS FROM MOUSE.

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 2)

No.	Name	Count	Type	Full Name
1	PCA	2	Mod. Amino Acid	PYROGLUTAMIC ACID

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	PCA	1	Mod. Amino Acid	PYROGLUTAMIC ACID

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	PCA	1	Mod. Amino Acid	PYROGLUTAMIC ACID

(no "Site" information available for 1T04)

Asymmetric Unit

No.	Residues
1	A:23	-	A:88
2	A:134	-	A:194
3	B:22	-	B:96
4	B:144	-	B:200
5	C:23	-	C:88
6	C:134	-	C:194
7	D:22	-	D:96
8	D:144	-	D:200

Asymmetric Unit

No.	Residues
1	Ser A:7	-	Pro A:8
2	Tyr A:94	-	Pro A:95
3	Tyr A:140	-	Pro A:141
4	Phe B:150	-	Pro B:151
5	Glu B:152	-	Pro B:153
6	Ser C:7	-	Pro C:8
7	Tyr C:94	-	Pro C:95
8	Tyr C:140	-	Pro C:141
9	Phe D:150	-	Pro D:151
10	Glu D:152	-	Pro D:153

(no "SAP(SNP)/Variant" information available for 1T04)

(no "PROSITE Motif" information available for 1T04)

(no "Exon" information available for 1T04)

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 A from PDB  Type:PROTEIN  Length:214
                                                                                                                                                                                                                                                      
               SCOP domains d1t04a1 A:1-108 Immunoglobulin light chain kappa variable domain, VL-kappa                                  d1t04a2 A:109-214 Immunoglobulin light chain kappa constant domain, CL-kappa                               SCOP domains
               CATH domains 1t04A01 A:1-107 Immunoglobulins                                                                            1t04A02 A:108-211 Immunoglobulins                                                                       --- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee......eeeeee.......eeeeee......ee.ee...ee.......eeeeee..eeeeee.........eeeeee......ee...eeeee.......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhhh..eeeeeee.......eeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1t04 A   1 DIQMTQSPSTLSASVGDRVTITCKASENVDTYVSWYQQKPGKAPKLLIYGASNRYTGVPSRFSGSGSGTDFTLTISSLQPDDFATYYCGQSYNYPFTFGQGTKVEVKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC 214
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210

Chain B from PDB  Type:PROTEIN  Length:219
                                                                                                                                                                                                                                                           
               SCOP domains d1t04b1 B:1-118 Immunoglobulin heavy chain variable domain, VH                                                        d1t04b2 B:119-219 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                       SCOP domains
               CATH domains -1t04B01 B:2-117 Immunoglobulins                                                                                     1t04B02 B:118-217 Immunoglobulins                                                                   -- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee..hhhhheeeeeee......eeeeee......eee.hhhh..eeeeee....eeeeee...hhhhheeeeeeee....eeee...eeeee...........ee..........eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhhhh...eeeeeehhhheeeeee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1t04 B   1 xVQLVQSGAELKKPGSSVKVSCKASGYIFTSSWINWVKQAPGQGLEWIGRIDPSDGEVHYNQDFKDKATLTVDKSTNTAYMELSSLRSEDTAVYYCARGFLPWFADWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKS 219
                            |       10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210         
                            1-PCA

Chain C from PDB  Type:PROTEIN  Length:214
                                                                                                                                                                                                                                                      
               SCOP domains d1t04c1 C:1-108 Immunoglobulin light chain kappa variable domain, VL-kappa                                  d1t04c2 C:109-214 Immunoglobulin light chain kappa constant domain, CL-kappa                               SCOP domains
               CATH domains 1t04C01 C:1-107 Immunoglobulins                                                                            1t04C02 C:108-211 Immunoglobulins                                                                       --- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee..eeee......eeeee........eeeeee......eeeee...ee.......eeeeee..eeeeee.........eeeeee......ee...eeeee.......eeeee..hhhhhh..eeeeeeeeeee....eeeeeee..ee....eeeee.........eeeeeeeeeehhhhhh..eeeeeeee......eeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1t04 C   1 DIQMTQSPSTLSASVGDRVTITCKASENVDTYVSWYQQKPGKAPKLLIYGASNRYTGVPSRFSGSGSGTDFTLTISSLQPDDFATYYCGQSYNYPFTFGQGTKVEVKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC 214
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210

Chain D from PDB  Type:PROTEIN  Length:219
                                                                                                                                                                                                                                                           
               SCOP domains d1t04d1 D:1-118 Immunoglobulin heavy chain variable domain, VH                                                        d1t04d2 D:119-219 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                       SCOP domains
               CATH domains -1t04D01 D:2-117 Immunoglobulins                                                                                     1t04D02 D:118-217 Immunoglobulins                                                                   -- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee..hhhhheeeeeee......eeeeee......eee.......eeeeeehhh.eeeeee...hhhhheeeeeeee....eeee...eeeee........eeeee..........eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhh.....eeeeeehhhheeeeee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1t04 D   1 xVQLVQSGAELKKPGSSVKVSCKASGYIFTSSWINWVKQAPGQGLEWIGRIDPSDGEVHYNQDFKDKATLTVDKSTNTAYMELSSLRSEDTAVYYCARGFLPWFADWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKS 219
                            |       10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210         
                            1-PCA

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(

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Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Immunoglobulin-like (3897)

Homologous Superfamily: Immunoglobulins (2282)

Human (Homo sapiens) (912)

1a	1t04A02	A:108-211
1b	1t04B01	B:2-117
1c	1t04D01	D:2-117
1d	1t04B02	B:118-217
1e	1t04D02	D:118-217
1f	1t04C02	C:108-211
1g	1t04A01	A:1-107
1h	1t04C01	C:1-107

(no "Pfam Domain" information available for 1T04)

Asymmetric Unit(hide GO term definitions)

(no "Gene Ontology" information available for 1T04)

Asymmetric Unit
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	Sites
(no "Sites" information available for 1t04)

	Cis Peptide Bonds
		Glu B:152 - Pro B:153	[ RasMol ]
		Glu D:152 - Pro D:153	[ RasMol ]
		Phe B:150 - Pro B:151	[ RasMol ]
		Phe D:150 - Pro D:151	[ RasMol ]
		Ser A:7 - Pro A:8	[ RasMol ]
		Ser C:7 - Pro C:8	[ RasMol ]
		Tyr A:140 - Pro A:141	[ RasMol ]
		Tyr A:94 - Pro A:95	[ RasMol ]
		Tyr C:140 - Pro C:141	[ RasMol ]
		Tyr C:94 - Pro C:95	[ RasMol ]

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

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	1t04
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1b2w	HUMANIZED FAB OF AN ANTI-GAMMA-INTERFERON ANTIBODY
1b4j	CHIMERIC FAB OF AN ANTI-GAMMA-INTERFERON ANTIBODY

Description

Compounds

Structural Features

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Ligands, Modified Residues, Ions (1, 2)

Sites (0, 0)

SS Bonds (8, 8)

Cis Peptide Bonds (10, 10)

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SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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SCOP Domains (4, 8)

CATH Domains (1, 8)

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