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(-) Description

Title :  CRYSTAL STRUCTURE OF FAB FRAGMENT COMPLEXED WITH GIBBERELLIN A4
 
Authors :  T. Murata, S. Fushinobu, M. Nakajima, O. Asami, T. Sassa, T. Wakagi, I. Y
Date :  20 Nov 01  (Deposition) - 11 Sep 02  (Release) - 25 Sep 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  H,I,L,M
Biol. Unit 1:  H,L  (1x)
Biol. Unit 2:  I,M  (1x)
Biol. Unit 3:  H (1x),I (1x),L (1x),M (1x)
Keywords :  Immunoglobuiln Fold, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Murata, S. Fushinobu, M. Nakajima, O. Asami, T. Sassa, T. Wakagi, I. Yamaguchi
Crystal Structure Of The Liganded Anti-Gibberellin A(4) Antibody 4-B8(8)/E9 Fab Fragment.
Biochem. Biophys. Res. Commun. V. 293 489 2002
PubMed-ID: 12054627  |  Reference-DOI: 10.1016/S0006-291X(02)00225-5
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - MONOCLONAL ANTIBODY LIGHT CHAIN
    Chains: L, M
    Engineered: YES
    Expression System: MUS MUSCULUS
    Expression System Cell: HYBRIDOMA CELL
    Expression System Cellular Location: ASCITIC FLUID
    Expression System Common: MOUSE
    Expression System Taxid: 10090
    Fragment: RESIDUES 1-217
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
 
Molecule 2 - MONOCLONAL ANTIBODY HEAVY CHAIN
    Chains: H, I
    Engineered: YES
    Expression System: MUS MUSCULUS
    Expression System Cell: HYBRIDOMA CELL
    Expression System Cellular Location: ASCITIC FLUID
    Expression System Common: MOUSE
    Expression System Taxid: 10090
    Fragment: VARIABLE DOMAIN, CONSTANT DOMAIN 1
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : HILM
Biological Unit 1 (1x): H L 
Biological Unit 2 (1x):  I M
Biological Unit 3 (1x): H (1x)I (1x)L (1x)M (1x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1GA42Ligand/IonGIBBERELLIN A4
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1GA41Ligand/IonGIBBERELLIN A4
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1GA41Ligand/IonGIBBERELLIN A4
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1GA41Ligand/IonGIBBERELLIN A4

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR H:32 , ALA H:33 , THR H:52 , THR H:53 , GLU H:99 , LEU H:102BINDING SITE FOR RESIDUE GA4 H 300
2AC2SOFTWARESER I:31 , THR I:52 , THR I:53 , ARG I:55 , LEU I:102 , LEU I:103BINDING SITE FOR RESIDUE GA4 I 1300

(-) SS Bonds  (8, 8)

Asymmetric Unit
No.Residues
1H:22 -H:96
2H:153 -H:208
3I:22 -I:96
4I:153 -I:208
5L:23 -L:93
6L:139 -L:199
7M:23 -M:93
8M:139 -M:199

(-) Cis Peptide Bonds  (12, 12)

Asymmetric Unit
No.Residues
1Thr L:7 -Pro L:8
2Val L:99 -Pro L:100
3Tyr L:145 -Pro L:146
4Phe H:159 -Pro H:160
5Glu H:161 -Pro H:162
6Arg H:201 -Pro H:202
7Thr M:7 -Pro M:8
8Val M:99 -Pro M:100
9Tyr M:145 -Pro M:146
10Phe I:159 -Pro I:160
11Glu I:161 -Pro I:162
12Arg I:201 -Pro I:202

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1KFA)

(-) 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 H from PDB  Type:PROTEIN  Length:213
                                                                                                                                                                                                                                                     
               SCOP domains d1kfah1 H:2-121 Immunoglobulin heavy chain variable domain, VH                                                         d1kfah2 H:127-227 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                SCOP domains
               CATH domains 1kfaH01 H:2-121 Immunoglobulins                                                                                        1kfaH02 H:127-225 Immunoglobulins                                                           -- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee...ee.....eeeeeeee..hhhhheeeeeee.....eeeeeee.....ee........eeeeee....eeeeee...hhhhheeeeeeee...............eeeee........eeeee...eeeeeeeeeee.....eeee.hhh....eee...ee....eeeeeeeeee.hhh.....eeeeee....eeeeee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1kfa H   2 VMLVESGGGLVKPGGSLKLSCAASGFTFSSYAMSWVRQTPERRLEWVATITTRGYTFYPDSVKGRFTVSRDNARNTLNLQMSSLRSEDTAMFYCTREGLLLDYFTMDYWGQGTSVTVSSAKTTPPSVYPLAPSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSSRPSETVTCNVAHPASSTKVDKKIVPAD 227
                                    11        21        31        41        51 ||     62        72        82        92       102       112       127       137 ||    154       164       174       184       194       204       214       224   
                                                                              53|                                                               121|         139|                                                                                
                                                                               55                                                                127          147                                                                                


Chain I from PDB  Type:PROTEIN  Length:209
                                                                                                                                                                                                                                                 
               SCOP domains d1kfai1 I:3-121 Immunoglobulin heavy chain variable domain, VH                                                        d1kfai2 I:127-225 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma             SCOP domains
               CATH domains 1kfaI01 I:3-121 Immunoglobulins                                                                                       1kfaI02 I:127-224 Immunoglobulins                                                         - CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee...ee.....eeeeeee...hhhhh.eeeeee.....eeeeeee.....ee.hhhhh..eeeeee....eeeeee...hhhhheeeeeeee........eeee...eeeee........eeeee...eeeeeeeeee.....eeee.hhh....eee...ee....eeeeeeeeehhhhh.....eeeeee....eeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1kfa I   3 MLVESGGGLVKPGGSLKLSCAASGFTFSSYAMSWVRQTPERRLEWVATITTRGYTFYPDSVKGRFTVSRDNARNTLNLQMSSLRSEDTAMFYCTREGLLLDYFTMDYWGQGTSVTVSSAKTTPPSVYPLAPMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSSRPSETVTCNVAHPASSTKVDKKIVP 225
                                    12        22        32        42        52||      63        73        83        93       103       113       128       138||     156       166       176       186       196       206       216         
                                                                             53|                                                               121|         139|                                                                             
                                                                              55                                                                127          148                                                                             


Chain L from PDB  Type:PROTEIN  Length:217
                                                                                                                                                                                                                                                         
               SCOP domains d1kfal1 L:1-112 Immunoglobulin light chain kappa variable domain, VL-kappa                                      d1kfal2 L:113-217 Immunoglobulin light chain kappa constant domain, CL-kappa                              SCOP domains
               CATH domains 1kfaL01 L:1-113 Immunoglobulins                                                                                  1kfaL02 L:114-215 Immunoglobulins                                                                     -- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee....eee....eeeeeee............eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeeee......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhh...eeeeeee.......eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1kfa L   1 DVVMTQTPLSLSVSLGDQASISCRSSQSLVHSNGNTYLHWYLQKPGQSPKLLIYKVSSRFSGFPDRFSGSGSGTDFTLKISRVEAEDLGVYFCSQSTHVPFTFGSGTKLEIKRADAGPTVSSFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHASYTCEAAHKTSTSPIAKSFNRA 217
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       


Chain M from PDB  Type:PROTEIN  Length:213
                                                                                                                                                                                                                                                     
               SCOP domains d1kfam1 M:1-112 Immunoglobulin light chain kappa variable domain, VL-kappa                                      d1kfam2 M:113-213 Immunoglobulin light chain kappa constant domain, CL-kappa                          SCOP domains
               CATH domains 1kfaM01 M:1-113 Immunoglobulins                                                                                  1kfaM02 M:114-213 Immunoglobulins                                                                    CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee............eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeeee........eee..hhhhhhh.eeeeeee.........eeeeee..eee...eeeee...........eeeeeeeehhhhhh...eeeeee.......eee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1kfa M   1 DVVMTQTPLSLSVSLGDQASISCRSSQSLVHSNGNTYLHWYLQKPGQSPKLLIYKVSSRFSGFPDRFSGSGSGTDFTLKISRVEAEDLGVYFCSQSTHVPFTFGSGTKLEIKRADAGPTVSSFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHASYTCEAAHKTSTSPIAKS 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 '|'

 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)
1a1kfaL02L:114-215
1b1kfaH02H:127-225
1c1kfaI02I:127-224
1d1kfaL01L:1-113
1e1kfaM01M:1-113
1f1kfaI01I:3-121
1g1kfaH01H:2-121
1h1kfaM02M:114-213

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

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

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