1NGW - JenaLib

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Title :   CHIMERIC AFFINITY MATURED FAB 7G12 COMPLEXED WITH MESOPORPHYRIN

Authors :   J. Yin, S. E. Andryski, A. E. Beuscher Iv, R. C. Stevens, P. G. Schultz

Date :   18 Dec 02 (Deposition) - 04 Feb 03 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.60

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

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

Reference :   J. Yin, S. E. Andryski, A. E. Beuscher Iv, R. C. Stevens, P. G. Schultz
Structural Evidence For Substrate Strain In Antibody Catalysis
Proc. Natl. Acad. Sci. Usa V. 100 856 2003
PubMed-ID: 12552112 | Reference-DOI: 10.1073/PNAS.0235873100
(for further references see the PDB file header)

Molecule 1 - MATURE METAL CHELATASE CATALYTIC ANTIBODY, LIGHT CHAIN
	Chains	:	L, A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	GERMLINE FAB FRAGMENT
	Organism Common	:	HOUSE MOUSE, HUMAN
	Organism Scientific	:	MUS MUSCULUS, HOMO SAPIENS
	Organism Taxid	:	10090,9606
	Strain	:	,

Molecule 2 - MATURE METAL CHELATASE CATALYTIC ANTIBODY, HEAVY CHAIN
	Chains	:	H, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	GERMLINE FAB FRAGMENT
	Organism Common	:	HOUSE MOUSE, HUMAN
	Organism Scientific	:	MUS MUSCULUS, HOMO SAPIENS
	Organism Taxid	:	10090,9606
	Strain	:	,

		1	2	3	4
Asymmetric Unit	:	A	B	H	L
Biological Unit 1 (1x)	:			H	L
Biological Unit 2 (1x)	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 2)

No.	Name	Count	Type	Full Name
1	MMP	2	Ligand/Ion	N-METHYLMESOPORPHYRIN

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	MMP	1	Ligand/Ion	N-METHYLMESOPORPHYRIN

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	MMP	1	Ligand/Ion	N-METHYLMESOPORPHYRIN

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LEU A:46 , TYR A:49 , GLN A:89 , TYR A:91 , ARG B:99 , ASP B:100 , MET B:101 , MMP H:217	BINDING SITE FOR RESIDUE MMP B 217
2	AC2	SOFTWARE	MMP B:217 , ARG H:99 , ASP H:100 , TYR L:49 , TYR L:55 , GLN L:89 , TYR L:91	BINDING SITE FOR RESIDUE MMP H 217

Asymmetric Unit

No.	Residues
1	A:23	-	A:88
2	A:134	-	A:194
3	B:22	-	B:96
4	B:141	-	B:197
5	H:22	-	H:96
6	H:141	-	H:197
7	L:23	-	L:88
8	L:134	-	L:194

Asymmetric Unit

No.	Residues
1	Thr L:7	-	Pro L:8
2	Tyr L:94	-	Pro L:95
3	Tyr L:140	-	Pro L:141
4	Phe H:147	-	Pro H:148
5	Glu H:149	-	Pro H:150
6	Thr A:7	-	Pro A:8
7	Tyr A:94	-	Pro A:95
8	Tyr A:140	-	Pro A:141
9	Phe B:147	-	Pro B:148
10	Glu B:149	-	Pro B:150

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

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

(no "Exon" information available for 1NGW)

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 d1ngwa1 A:1-107 Immunoglobulin light chain kappa variable domain, VL-kappa                                 d1ngwa2 A:108-213 Immunoglobulin light chain kappa constant domain, CL-kappa                               SCOP domains
               CATH domains 1ngwA01 A:1-108 Immunoglobulins                                                                             1ngwA02 A:109-213 Immunoglobulins                                                                         CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee..eeeee....eeeeee........eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeeee......eeeee..hhhhhhh..eeeeeeeeee....eeeeeee..ee....eeeee.........eeeeeeeeehhhhhhhh.eeeeeeee......eeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ngw A   1 ELVMTQTPKFMSTTVGDRVSITCKASQNVGTPVAWYQQKPGQSPKLLIYSASNRYTGVPDRFTGSGSGTDFTLTISNMQSEDLADYFCQQYSSYPLTFGGGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRNE 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:216
 aligned with HVM49_MOUSE | P06328 from UniProtKB/Swiss-Prot  Length:117

    Alignment length:216
                                                                                                                           117                                                                                                                      
                                    29        39        49        59        69        79        89        99       109       | -         -         -         -         -         -         -         -         -         -         -         -      
          HVM49_MOUSE    20 PVQLQQPGAELVKPGASVKLSCKASGYTFTSYWMHWVKQRPGRGLEWIGNIDPNSGGTKYNEKFKSKATLTVDKPSSTAYMQLSSLTSEDSAVYYCTR----------------------------------------------------------------------------------------------------------------------   -
               SCOP domains d1ngwb1 B:1-114 Immunoglobulin heavy chain variable domain, VH                                                    d1ngwb2 B:115-216 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                        SCOP domains
               CATH domains 1ngwB01 B:1-114 Immunoglobulins                                                                                   1ngwB02 B:115-214 Immunoglobulins                                                                   -- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeee...eee.....eee.eeee........eeeee.......eeeeee......eee.......eeeeee....eeeeee...hhhhheeeeeee.........eeeee........eeeee..........eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhh....eeeeeeehhhheeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1ngw B   1 QVQLLESGAELVKPGASVKLSCKASGYTFTSYWMHWVKQRPGRGLEWIGMIDPNSGGTKYNEKFKSKATLTVDKPSNTAYMQLSSLTSEDSAVYYCTRRDMDYWGAGTTVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKIVPKS 216
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210

Chain H from PDB  Type:PROTEIN  Length:216
 aligned with HVM49_MOUSE | P06328 from UniProtKB/Swiss-Prot  Length:117

    Alignment length:216
                                                                                                                           117                                                                                                                      
                                    29        39        49        59        69        79        89        99       109       | -         -         -         -         -         -         -         -         -         -         -         -      
          HVM49_MOUSE    20 PVQLQQPGAELVKPGASVKLSCKASGYTFTSYWMHWVKQRPGRGLEWIGNIDPNSGGTKYNEKFKSKATLTVDKPSSTAYMQLSSLTSEDSAVYYCTR----------------------------------------------------------------------------------------------------------------------   -
               SCOP domains d1ngwh1 H:1-114 Immunoglobulin heavy chain variable domain, VH                                                    d1ngwh2 H:115-216 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                        SCOP domains
               CATH domains 1ngwH01 H:1-114 Immunoglobulins                                                                                   1ngwH02 H:115-214 Immunoglobulins                                                                   -- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeee...eee.....eee.eeee........eeeee.......eeeeee......eee.......eeeeee....eeeeee...hhhhheeeeeee.........eeeee........eeeee..........eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhh....eeeeeeehhhheeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1ngw H   1 QVQLLESGAELVKPGASVKLSCKASGYTFTSYWMHWVKQRPGRGLEWIGMIDPNSGGTKYNEKFKSKATLTVDKPSNTAYMQLSSLTSEDSAVYYCTRRDMDYWGAGTTVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKIVPKS 216
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210

Chain L from PDB  Type:PROTEIN  Length:213
                                                                                                                                                                                                                                                     
               SCOP domains d1ngwl1 L:1-107 Immunoglobulin light chain kappa variable domain, VL-kappa                                 d1ngwl2 L:108-213 Immunoglobulin light chain kappa constant domain, CL-kappa                               SCOP domains
               CATH domains 1ngwL01 L:1-108 Immunoglobulins                                                                             1ngwL02 L:109-213 Immunoglobulins                                                                         CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee..eeeee....eeeeee........eeeeee......eeeee...ee.......eeee....eeeeee...hhhhheeeeeee......ee...eeeeee......eeeee..hhhhhhh..eeeeeeeeee....eeeeeee..ee....eeeee.........eeeeeeeeehhhhhhhh.eeeeeeee......eeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ngw L   1 ELVMTQTPKFMSTTVGDRVSITCKASQNVGTPVAWYQQKPGQSPKLLIYSASNRYTGVPDRFTGSGSGTDFTLTISNMQSEDLADYFCQQYSSYPLTFGGGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRNE 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(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Immunoglobulin-like (3897)

Homologous Superfamily: Immunoglobulins (2282)

House mouse, human (Mus musculus, homo sapiens) (20)

1a	1ngwA02	A:109-213
1b	1ngwL02	L:109-213
1c	1ngwA01	A:1-108
1d	1ngwL01	L:1-108
1e	1ngwB01	B:1-114
1f	1ngwH01	H:1-114
1g	1ngwB02	B:115-214
1h	1ngwH02	H:115-214

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

Asymmetric Unit(hide GO term definitions)

Chain B,H (HVM49_MOUSE | P06328)

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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		Glu H:149 - Pro H:150	[ RasMol ]
		Phe B:147 - Pro B:148	[ RasMol ]
		Phe H:147 - Pro H:148	[ RasMol ]
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		Tyr L:94 - Pro L:95	[ RasMol ]

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Description

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Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (8, 8)

Cis Peptide Bonds (10, 10)

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