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(-) Description

Title :  IGG-FAB FRAGMENT OF ENGINEERED HUMAN MONOCLONAL ANTIBODY CTM01
 
Authors :  M. J. Banfield, R. L. Brady
Date :  24 Feb 97  (Deposition) - 25 Feb 98  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A,B,H,L
Biol. Unit 1:  H,L  (1x)
Biol. Unit 2:  A,B  (1x)
Biol. Unit 3:  A (1x),B (1x),H (1x),L (1x)
Keywords :  Immunoglobulin, Fab Fragment (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. J. Banfield, D. J. King, A. Mountain, R. L. Brady
Vl:Vh Domain Rotations In Engineered Antibodies: Crystal Structures Of The Fab Fragments From Two Murine Antitumor Antibodies And Their Engineered Human Constructs.
Proteins V. 29 161 1997 (for further references see the PDB file header)

(-) Compounds

Molecule 1 - IGG CTM01 FAB (LIGHT CHAIN)
    Chains: L, A
    Engineered: YES
    Expression System: MUS MUSCULUS
    Expression System Cell: NSO CELLS
    Expression System Common: HOUSE MOUSE
    Expression System Taxid: 10090
    Fragment: CTM01
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 2 - IGG CTM01 FAB (HEAVY CHAIN)
    Chains: H, B
    Engineered: YES
    Expression System: MUS MUSCULUS
    Expression System Cell: NSO CELLS
    Expression System Common: HOUSE MOUSE
    Expression System Taxid: 10090
    Fragment: CTM01
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABHL
Biological Unit 1 (1x):   HL
Biological Unit 2 (1x): AB  
Biological Unit 3 (1x): A (1x)B (1x)H (1x)L (1x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1SO41Ligand/IonSULFATE ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1SO4-1Ligand/IonSULFATE ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1SO41Ligand/IonSULFATE ION
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1SO41Ligand/IonSULFATE ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:189 , ASN A:209 , TYR B:27 , THR B:28 , PHE B:29 , THR B:30 , ASN B:76BINDING SITE FOR RESIDUE SO4 B 213

(-) SS Bonds  (10, 10)

Asymmetric Unit
No.Residues
1A:23 -A:88
2A:133 -A:193
3A:213 -B:127
4B:22 -B:92
5B:140 -B:196
6H:22 -H:92
7H:140 -H:196
8L:23 -L:88
9L:133 -L:193
10L:213 -H:127

(-) Cis Peptide Bonds  (10, 10)

Asymmetric Unit
No.Residues
1Ser L:7 -Pro L:8
2Tyr L:94 -Pro L:95
3Tyr L:139 -Pro L:140
4Phe H:146 -Pro H:147
5Glu H:148 -Pro H:149
6Ser A:7 -Pro A:8
7Tyr A:94 -Pro A:95
8Tyr A:139 -Pro A:140
9Phe B:146 -Pro B:147
10Glu B:148 -Pro B:149

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1AD9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1AD9)

(-) Exons   (0, 0)

(no "Exon" information available for 1AD9)

(-) Sequences/Alignments

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:219
                                                                                                                                                                                                                                                            
               SCOP domains d1ad9a1 A:1-107 Immunoglobulin light chain kappa variable domain, VL-kappa                                       d1ad9a2 A:108-213 Immunoglobulin light chain kappa constant domain, CL-kappa                               SCOP domains
               CATH domains 1ad9A01 A:1-107 Immunoglobulins                                                                                  1ad9A02 A:108-208 Immunoglobulins                                                                    ----- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee............eeeeee......eeeee............eeeeee..eeeeee....hhh..eeeeee............eeee.......eeeee...hhhhhh.eeeeeeeee.......eeeeee........................eeeeeeeehhhhh...eeeeeee.......eeeeeehhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1ad9 A    1 DIQMTQSPSTLSASVGDRVTITCRSSKSLLHSNGDTFLYWFQQKPGKAPKLLMYRMSNLASGVPSRFSGSGSGTEFTLTISSLQPDDFATYYCMQHLEYPFTFGQGTKVEVKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC  213
                                    10        20       27C||      35        45        55        65        75        85        95       105 |     114       124       134       144       154       164       174       184       194       204         
                                                     27A||||                                                                            106A                                                                                                           
                                                      27B|||                                                                                                                                                                                           
                                                       27C||                                                                                                                                                                                           
                                                        27D|                                                                                                                                                                                           
                                                         27E                                                                                                                                                                                           


Chain B from PDB  Type:PROTEIN  Length:219
                                                                                                                                                                                                                                                            
               SCOP domains d1ad9b1 B:1-113 Immunoglobulin heavy chain variable domain, VH                                                          d1ad9b2 B:114-212 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                     SCOP domains
               CATH domains 1ad9B01 B:1-113 Immunoglobulins                                                                                         1ad9B02 B:114-212 Immunoglobulins                                                                   CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee...hhh.eeeeeee.....eeeeeeee....eeee.hhh...eeeeee....eeeeee....hhh.eeeeeeee..............eeeee........eeeee..........eeeeeeeee.......eeeehhh.....eee............eeeeeeee........eeeeeeehhh.eeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1ad9 B    1 EIQLVQSGAEVKKPGSSVKVSCKASGYTFTDYYINWMRQAPGQGLEWIGWIDPGSGNTKYNEKFKGRATLTVDTSTNTAYMELSSLRSEDTAFYFCAREKTTYYYAMDYWGQGTLVTVSSASTKGPSVFPLAPCSRSTSESTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTKTYTCNVDHKPSNTKVDKRVE  212
                                    10        20        30        40        50  |     59        69        79   |||  86        96    |||103       113       123       133       143       153       163       173       183       193       203         
                                                                              52A                            82A||               100A||                                                                                                                
                                                                                                              82B|                100B|                                                                                                                
                                                                                                               82C                 100C                                                                                                                


Chain H from PDB  Type:PROTEIN  Length:219
                                                                                                                                                                                                                                                            
               SCOP domains d1ad9h1 H:1-113 Immunoglobulin heavy chain variable domain, VH                                                          d1ad9h2 H:114-212 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                     SCOP domains
               CATH domains 1ad9H01 H:1-113 Immunoglobulins                                                                                         1ad9H02 H:114-212 Immunoglobulins                                                                   CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee...hhh.eeeeeee.....eeeeeeee....eeee.hhh...eeeeee....eeeeee....hhh.eeeeeeee..............eeeee........eeeee..........eeeeeeeee...........hhh.....eee............eeeeeeee........eeeeeeehhh.eeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1ad9 H    1 EIQLVQSGAEVKKPGSSVKVSCKASGYTFTDYYINWMRQAPGQGLEWIGWIDPGSGNTKYNEKFKGRATLTVDTSTNTAYMELSSLRSEDTAFYFCAREKTTYYYAMDYWGQGTLVTVSSASTKGPSVFPLAPCSRSTSESTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTKTYTCNVDHKPSNTKVDKRVE  212
                                    10        20        30        40        50  |     59        69        79   |||  86        96    |||103       113       123       133       143       153       163       173       183       193       203         
                                                                              52A                            82A||               100A||                                                                                                                
                                                                                                              82B|                100B|                                                                                                                
                                                                                                               82C                 100C                                                                                                                


Chain L from PDB  Type:PROTEIN  Length:219
                                                                                                                                                                                                                                                            
               SCOP domains d1ad9l1 L:1-107 Immunoglobulin light chain kappa variable domain, VL-kappa                                       d1ad9l2 L:108-213 Immunoglobulin light chain kappa constant domain, CL-kappa                               SCOP domains
               CATH domains 1ad9L01 L:1-106 Immunoglobulins                                                                                -1ad9L02 L:107-210 Immunoglobulins                                                                       --- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee............eeeeee......eeeee............eeeeee..eeeeee....hhh..eeeeee............eeee.......eeeee...hhhhhh.eeeeeeeee.......eeeeee........................eeeeeeeehhhhh...eeeeeee.......eeeeeehhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1ad9 L    1 DIQMTQSPSTLSASVGDRVTITCRSSKSLLHSNGDTFLYWFQQKPGKAPKLLMYRMSNLASGVPSRFSGSGSGTEFTLTISSLQPDDFATYYCMQHLEYPFTFGQGTKVEVKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC  213
                                    10        20       27C||      35        45        55        65        75        85        95       105 |     114       124       134       144       154       164       174       184       194       204         
                                                     27A||||                                                                            106A                                                                                                           
                                                      27B|||                                                                                                                                                                                           
                                                       27C||                                                                                                                                                                                           
                                                        27D|                                                                                                                                                                                           
                                                         27E
   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 '|'

 Classification and Annotation

(-) SCOP Domains  (4, 8)

Asymmetric Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 8)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)
(-)
Architecture: Sandwich (5577)
(-)
Topology: Immunoglobulin-like (3897)
(-)
Homologous Superfamily: Immunoglobulins (2282)
(-)
Human (Homo sapiens) (912)
1a1ad9A02A:108-208
1b1ad9B02B:114-212
1c1ad9H02H:114-212
1d1ad9B01B:1-113
1e1ad9H01H:1-113
1f1ad9L02L:107-210
1g1ad9L01L:1-106
1h1ad9A01A:1-107

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1AD9)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 1AD9)

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  1ad9
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 Related Entries

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