2ORB - JenaLib

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Title :   THE STRUCTURE OF THE ANTI-C-MYC ANTIBODY 9E10 FAB FRAGMENT

Authors :   N. Krauss, P. Scheerer, W. Hoehne

Date :   02 Feb 07 (Deposition) - 12 Feb 08 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

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

Keywords :   Antigen-Antibody Complex, Antigen Recognition, Long Cdr H3, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   N. Krauss, H. Wessner, K. Welfle, H. Welfle, C. Scholz, M. Seifert, K. Zubow, J. Ay, M. Hahn, P. Scheerer, A. Skerra, W. Hohne
The Structure Of The Anti-C-Myc Antibody 9E10 Fab Fragment/Epitope Peptide Complex Reveals A Novel Binding Mode Dominated By The Heavy Chain Hypervariable Loops.
Proteins V. 73 552 2008
PubMed-ID: 18473392 | Reference-DOI: 10.1002/PROT.22080

Molecule 1 - MONOCLONAL ANTI-C-MYC ANTIBODY 9E10
	Chains	:	L, M
	Fragment	:	LIGHT CHAIN OF ANTIGEN BINDING FRAGMENT, FAB
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Strain	:	BALB/C

Molecule 2 - MONOCLONAL ANTI-C-MYC ANTIBODY 9E10
	Chains	:	H, I
	Fragment	:	HEAVY CHAIN OF ANTIGEN BINDING FRAGMENT, FAB
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Strain	:	BALB/C

		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)

Asymmetric Unit (1, 2)

No.	Name	Count	Type	Full Name
1	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	SO4	-1	Ligand/Ion	SULFATE ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	PHE H:27 , THR H:28 , TYR H:32	BINDING SITE FOR RESIDUE SO4 H 301
2	AC2	SOFTWARE	LYS H:143 , GLY H:144 , GLN H:171 , LEU H:174 , THR H:176 , HOH H:328 , ASP M:184	BINDING SITE FOR RESIDUE SO4 H 302

Asymmetric Unit

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

Asymmetric Unit

No.	Residues
1	Ser L:7	-	Pro L:8
2	His L:76	-	Pro L:77
3	Val L:94	-	Pro L:95
4	Tyr L:140	-	Pro L:141
5	Phe H:146	-	Pro H:147
6	Glu H:148	-	Pro H:149
7	Trp H:188	-	Pro H:189
8	Ser M:7	-	Pro M:8
9	His M:76	-	Pro M:77
10	Val M:94	-	Pro M:95
11	Tyr M:140	-	Pro M:141
12	Phe I:146	-	Pro I:147
13	Glu I:148	-	Pro I:149
14	Trp I:188	-	Pro I:189

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

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

(no "Exon" information available for 2ORB)

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:212
                                                                                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------d2orbh1 H:114-212 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma             -- SCOP domains
               CATH domains 2orbH01 H:1-113 Immunoglobulins                                                                                       2orbH02 H:114-211 Immunoglobulins                                                          --- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..eee.....eeeeeeee..hhhhh.eeeeee.....eeeeeee......ee........eeeeee....eeeeee...hhhhheeeeeeee.....eeee...eeeee........eeeee...eeeeeeeeeee.....eeee.hhh....eee...ee....eeeeeeeeee.........eeeeeehhhheeeeee..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2orb H    1 EVHLVESGGDLVKPGGSLKLSCAASGFTFSHYGMSWVRQTPDKRLEWVATIGSRGTYTHYPDSVKGRFTISRDNDKNALYLQMNSLKSEDTAMYYCARRSEYSAMDYWGQGASVTVSSAKTTPPSVYPLAPSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPRD  214
                                    10        20        30        40        50  |     59        69        79   |||  86        96|||||  105       115       125||     142       152       162       172       182       192       202       212  
                                                                              52A                            82A||             97||||                       126|                                                                                
                                                                                                              82B|            100G|||                        134                                                                                
                                                                                                               82C             100H||                                                                                                           
                                                                                                                                100I|                                                                                                           
                                                                                                                                 100J

Chain I from PDB  Type:PROTEIN  Length:209
                                                                                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------d2orbi1 I:114-212 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma             -- SCOP domains
               CATH domains 2orbI01 I:1-113 Immunoglobulins                                                                                    2orbI02 I:114-211 Immunoglobulins                                                          --- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..eee.....eeeeeeee..hhhhh.eeeeee.....eeeeeee......ee........eeeeee....eeeeee...hhhhheeeeeee.....ee...eeeee........eeeee...eeeeeeeeeee.....eeee.hhh....eee...ee....eeeeeeeeee.........eeeeeehhhheeeeee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2orb I    1 EVHLVESGGDLVKPGGSLKLSCAASGFTFSHYGMSWVRQTPDKRLEWVATIGSRGTYTHYPDSVKGRFTISRDNDKNALYLQMNSLKSEDTAMYYCARRSAMDYWGQGASVTVSSAKTTPPSVYPLAPSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPRD  214
                                    10        20        30        40        50  |     59        69        79   |||  86        96||     108       118       135       145       155       165       175       185       195       205         
                                                                              52A                            82A||            96||                       126|                                                                                
                                                                                                              82B|           100I|                        134                                                                                
                                                                                                               82C            100J

Chain L from PDB  Type:PROTEIN  Length:212
 aligned with KV3A1_MOUSE | P01654 from UniProtKB/Swiss-Prot  Length:111

    Alignment length:216
                                                                                                                                        111                                                                                                         
                                    10        20        30        40        50        60        70        80        90       100       110|        -         -         -         -         -         -         -         -         -         -      
         KV3A1_MOUSE      1 DIVLTQSPASLAVSLGQRATISCRASESVDNYGISFMNWFQQKPGQPPKLLIYAASNQGSGVPARFSGSGSGTDFSLNIHPMEEDDTAMYFCQQSKEVPWTFGGGTKLEIK---------------------------------------------------------------------------------------------------------    -
               SCOP domains d2orbl1 L:1-107 automated matc    hes                                                                          d2orbl2 L:108-212 automated matches                                                                       SCOP domains
               CATH domains 2orbL01 L:1-108 Immunoglobulin    s                                                                             2orbL02 L:109-212 Immunoglobulins                                                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee.....----..eeeeee......eeeee...ee.......eeeee...eeeeee........eeeeeee......ee...eeeeee......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhhhh.eeeeeee.......eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                2orb L    1 DIVLTQSPASLAVSLGQRATISCRASESVD----SFMNWFQQKPGQPPKLLIYAISNRGSGVPARFSGSGSGTDFSLNIHPVEEDDPAMYFCQQTKEVPWTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRN  212
                                    10        20       27C    |   36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206      
                                                     27A||   31                                                                                                                                                                                     
                                                      27B|                                                                                                                                                                                          
                                                       27C

Chain M from PDB  Type:PROTEIN  Length:210
 aligned with KV3A1_MOUSE | P01654 from UniProtKB/Swiss-Prot  Length:111

    Alignment length:217
                                                                                                                                        111                                                                                                          
                                    10        20        30        40        50        60        70        80        90       100       110|        -         -         -         -         -         -         -         -         -         -       
         KV3A1_MOUSE      1 DIVLTQSPASLAVSLGQRATISCRASESVDNYGISFMNWFQQKPGQPPKLLIYAASNQGSGVPARFSGSGSGTDFSLNIHPMEEDDTAMYFCQQSKEVPWTFGGGTKLEIK----------------------------------------------------------------------------------------------------------    -
               SCOP domains d2orbm1 M:1-107 automated matc      hes                                                                        d2orbm2 M:108-213 automated matches                                                                        SCOP domains
               CATH domains 2orbM01 M:1-108 Immunoglobulin      s                                                                           2orbM02 M:109-213 Immunoglobulins                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee.....------.eeeee......eeeee...ee.......eeeee...eeeeee........eeeeeee.-....ee...eeeeee......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhhhh.eeeeeee.......eeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2orb M    1 DIVLTQSPASLAVSLGQRATISCRASESVD------MNWFQQKPGQPPKLLIYAISNRGSGVPARFSGSGSGTDFSLNIHPVEEDDPAMYFCQQT-EVPWTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNE  213
                                    10        20       27C      | 36        46        56        66        76        86    | | 96       106       116       126       136       146       156       166       176       186       196       206       
                                                     27A||     33                                                        91 |                                                                                                                        
                                                      27B|                                                                 93                                                                                                                        
                                                       27C

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 (Mus musculus) (616)

1a	2orbM02	M:109-213
1b	2orbH02	H:114-211
1c	2orbI02	I:114-211
1d	2orbM01	M:1-108
1e	2orbL01	L:1-108
1f	2orbI01	I:1-113
1g	2orbH01	H:1-113
1h	2orbL02	L:109-212

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

Asymmetric Unit(hide GO term definitions)

Chain L,M (KV3A1_MOUSE | P01654)

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.

Asymmetric Unit
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	Sites
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	Cis Peptide Bonds
		Glu H:148 - Pro H:149	[ RasMol ]
		Glu I:148 - Pro I:149	[ RasMol ]
		His L:76 - Pro L:77	[ RasMol ]
		His M:76 - Pro M:77	[ RasMol ]
		Phe H:146 - Pro H:147	[ RasMol ]
		Phe I:146 - Pro I:147	[ RasMol ]
		Ser L:7 - Pro L:8	[ RasMol ]
		Ser M:7 - Pro M:8	[ 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 ]
		Val L:94 - Pro L:95	[ RasMol ]
		Val M:94 - Pro M:95	[ RasMol ]

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	KV3A1_MOUSE \| P01654	:	1mf2 1ok5 2or9

2or9	STRUCTURE OF THE SAME FAB IN COMPLEX WITH ITS EPITOPE PEPTIDE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (8, 8)

Cis Peptide Bonds (14, 14)

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