3L7F - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Title :   STRUCTURE OF IL-13 ANTIBODY H2L6, A HUMANIZED VARIANT OF C836

Authors :   A. Teplyakov, G. Obmolova, T. Malia, G. L. Gilliland

Date :   28 Dec 09 (Deposition) - 10 Nov 10 (Release) - 10 Nov 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.60

Chains :   Asym. Unit : A,B,D,E,H,L
Biol. Unit 1: H,L  (1x)
Biol. Unit 2: A,B  (1x)
Biol. Unit 3: D,E  (1x)

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

Reference :   J. Fransson, A. Teplyakov, G. Raghunathan, E. Chi, W. Cordier, T. Dinh Y. Feng, J. Giles-Komar, G. Gilliland, B. Lollo, T. J. Malia, W. Nishioka, G. Obmolova, S. Zhao, Y. Zhao, R. V. Swanson, J. C. Almagro
Human Framework Adaptation Of A Mouse Anti-Human Il-13 Antibody.
J. Mol. Biol. V. 398 214 2010
PubMed-ID: 20226193 | Reference-DOI: 10.1016/J.JMB.2010.03.004

Molecule 1 - H2L6 LIGHT CHAIN
	Chains	:	L, A, D
	Engineered	:	YES
	Expression System	:	HOMO SAPIENS
	Expression System Cell	:	HUMAN EMBRYONIC KIDNEY (HEK) 293 CELLS
	Expression System Common	:	HUMAN
	Expression System Taxid	:	9606
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

Molecule 2 - H2L6 HEAVY CHAIN
	Chains	:	H, B, E
	Engineered	:	YES
	Expression System	:	HOMO SAPIENS
	Expression System Cell	:	HUMAN EMBRYONIC KIDNEY (HEK) 293 CELLS
	Expression System Common	:	HUMAN
	Expression System Taxid	:	9606
	Fragment	:	FD FRAGMENT OF THE HEAVY CHAIN, VH AND CH1 DOMAINS
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

		1	2	3	4	5	6
Asymmetric Unit	:	A	B	D	E	H	L
Biological Unit 1 (1x)	:					H	L
Biological Unit 2 (1x)	:	A	B
Biological Unit 3 (1x)	:			D	E

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 7)

No.	Name	Count	Type	Full Name
1	CA	1	Ligand/Ion	CALCIUM ION
2	PCA	3	Mod. Amino Acid	PYROGLUTAMIC ACID
3	SO4	3	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 3)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	PCA	1	Mod. Amino Acid	PYROGLUTAMIC ACID
3	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	PCA	1	Mod. Amino Acid	PYROGLUTAMIC ACID
3	SO4	-1	Ligand/Ion	SULFATE ION

Biological Unit 3 (2, 2)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	PCA	1	Mod. Amino Acid	PYROGLUTAMIC ACID
3	SO4	1	Ligand/Ion	SULFATE ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG H:60 , TYR H:61 , TYR L:94	BINDING SITE FOR RESIDUE SO4 H 1001
2	AC2	SOFTWARE	GLY A:66 , SER A:67 , GLY D:66 , SER D:67 , GLY L:66 , SER L:67 , HOH L:221 , HOH L:222 , HOH L:225	BINDING SITE FOR RESIDUE SO4 L 1002
3	AC3	SOFTWARE	ASN D:92 , TYR D:96 , ARG L:18	BINDING SITE FOR RESIDUE SO4 D 1003
4	AC4	SOFTWARE	THR D:69 , ASP D:70 , HOH D:219 , HOH D:232 , HOH D:238	BINDING SITE FOR RESIDUE CA D 1004

Asymmetric Unit

No.	Residues
1	A:23	-	A:88
2	A:134	-	A:194
3	B:22	-	B:97
4	B:148	-	B:204
5	D:23	-	D:88
6	D:134	-	D:194
7	E:22	-	E:97
8	E:148	-	E:204
9	H:22	-	H:97
10	H:148	-	H:204
11	L:23	-	L:88
12	L:134	-	L:194

Asymmetric Unit

No.	Residues
1	Ser L:7	-	Pro L:8
2	Tyr L:94	-	Pro L:95
3	Tyr L:140	-	Pro L:141
4	Phe H:154	-	Pro H:155
5	Glu H:156	-	Pro H:157
6	Ser A:7	-	Pro A:8
7	Tyr A:94	-	Pro A:95
8	Tyr A:140	-	Pro A:141
9	Phe B:154	-	Pro B:155
10	Glu B:156	-	Pro B:157
11	Ser D:7	-	Pro D:8
12	Tyr D:94	-	Pro D:95
13	Tyr D:140	-	Pro D:141
14	Phe E:154	-	Pro E:155
15	Glu E:156	-	Pro E:157

(no "SAP(SNP)/Variant" information available for 3L7F)

(no "PROSITE Motif" information available for 3L7F)

(no "Exon" information available for 3L7F)

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:213
                                                                                                                                                                                                                                                     
               SCOP domains d3l7fa1 A:1-107 automated matches                                                                          d3l7fa2 A:108-213 automated matches                                                                        SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee...........eeeee.......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee........eeeee.........eeeeeeeeeehhhhh...eeeeeee.......eeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3l7f A   1 EIVLTQSPATLSLSPGERATLSCRASKSISKYLAWYQQKPGQAPRLLIYSGSTLQSGIPARFSGSGSGTDFTLTISSLEPEDFAVYYCQQHNEYPYTFGQGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGE 213
                                    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:221
                                                                                                                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee....ee.....eeeeeeee.........eeeeeee......eeeeeee....eee...hhh.eeeeeehhh.eeeeee...hhhhheeeeeeee.......eeee...eeeee........eeeee..........eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhhhhh..eeeeee....eeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3l7f B   1 xVTLKESGPVLVKPTETLTLTCTVSGFSLSTYGMGVGWIRQPPGKALEWLAHIWWDDVKRYNPALKSRLTISKDTSKSQVVLTMTNMDPVDTATYYCARMGSDYDVWFDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEP 221
                            |       10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220 
                            1-PCA

Chain D from PDB  Type:PROTEIN  Length:213
                                                                                                                                                                                                                                                     
               SCOP domains d3l7fd1 D:1-107 automated matches                                                                          d3l7fd2 D:108-213 automated matches                                                                        SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee...........eeeee..............hhhhhh..eeeeeee........eeeeeee..ee....eeeee...........eeeeeeeehhhhh...eeeeeeee......eeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3l7f D   1 EIVLTQSPATLSLSPGERATLSCRASKSISKYLAWYQQKPGQAPRLLIYSGSTLQSGIPARFSGSGSGTDFTLTISSLEPEDFAVYYCQQHNEYPYTFGQGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGE 213
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210

Chain E from PDB  Type:PROTEIN  Length:221
                                                                                                                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee....ee.....eeeeeeee.........eeeeeee......eeeeeee....eee...hhh.eeeeeehhh.eeeeee...hhhhheeeeeeee.......eeee...eeeee........eeeee..........eeeeeeeeeee.....eeee.hhh..........ee.....eeeeeeeeee.hhhh...eeeeeeehhhheeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3l7f E   1 xVTLKESGPVLVKPTETLTLTCTVSGFSLSTYGMGVGWIRQPPGKALEWLAHIWWDDVKRYNPALKSRLTISKDTSKSQVVLTMTNMDPVDTATYYCARMGSDYDVWFDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEP 221
                            |       10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220 
                            1-PCA

Chain H from PDB  Type:PROTEIN  Length:222
                                                                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee.........eeeeeee......eeeeeee....eee...hhh.eeeeee....eeeeee...hhhhheeeeeeee.......eeee...eeeee........eeeee..hhhhh...eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhh....eeeeeeehhhheeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3l7f H   1 xVTLKESGPVLVKPTETLTLTCTVSGFSLSTYGMGVGWIRQPPGKALEWLAHIWWDDVKRYNPALKSRLTISKDTSKSQVVLTMTNMDPVDTATYYCARMGSDYDVWFDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPK 222
                            |       10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220  
                            1-PCA

Chain L from PDB  Type:PROTEIN  Length:213
                                                                                                                                                                                                                                                     
               SCOP domains d3l7fl1 L:1-107 automated matches                                                                          d3l7fl2 L:108-213 automated matches                                                                        SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeee.......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhhh..eeeeeee.......eeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3l7f L   1 EIVLTQSPATLSLSPGERATLSCRASKSISKYLAWYQQKPGQAPRLLIYSGSTLQSGIPARFSGSGSGTDFTLTISSLEPEDFAVYYCQQHNEYPYTFGQGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGE 213
                                    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)

Human (Homo sapiens) [TaxId: 9606] (448)

1a	d3l7fa1	A:1-107
1b	d3l7fd1	D:1-107
1c	d3l7fl1	L:1-107

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

Protein domain: automated matches (652)

Human (Homo sapiens) [TaxId: 9606] (334)

2a	d3l7fa2	A:108-213
2b	d3l7fd2	D:108-213
2c	d3l7fl2	L:108-213

(no "CATH Domain" information available for 3L7F)

(no "Pfam Domain" information available for 3L7F)

Asymmetric Unit(hide GO term definitions)

(no "Gene Ontology" information available for 3L7F)

Asymmetric Unit
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	Ligands, Modified Residues, Ions
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	Sites
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		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Glu B:156 - Pro B:157	[ RasMol ]
		Glu E:156 - Pro E:157	[ RasMol ]
		Glu H:156 - Pro H:157	[ RasMol ]
		Phe B:154 - Pro B:155	[ RasMol ]
		Phe E:154 - Pro E:155	[ RasMol ]
		Phe H:154 - Pro H:155	[ RasMol ]
		Ser A:7 - Pro A:8	[ RasMol ]
		Ser D:7 - Pro D:8	[ RasMol ]
		Ser L:7 - Pro L:8	[ RasMol ]
		Tyr A:140 - Pro A:141	[ RasMol ]
		Tyr A:94 - Pro A:95	[ RasMol ]
		Tyr D:140 - Pro D:141	[ RasMol ]
		Tyr D:94 - Pro D:95	[ RasMol ]
		Tyr L:140 - Pro L:141	[ RasMol ]
		Tyr L:94 - Pro L:95	[ RasMol ]

Biological Units
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		Biological Unit 3	[ Jena3D ]

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	3l7f
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3l5w	IL-13:C836 FAB COMPLEX
3l5x	IL-13:H2L6 FAB COMPLEX
3l5y	IL-13:M1295 FAB COMPLEX
3l7e

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 7)

Sites (4, 4)

SS Bonds (12, 12)

Cis Peptide Bonds (15, 15)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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