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(-) Description

Title :  CRYSTAL STRUCTURE OF A FAB FRAGMENT WITH ITS LIGAND PEPTIDE
 
Authors :  Y. Kitago, K. K. Kaneko, S. Ogasawara, Y. Kato, J. Takagi
Date :  24 Jun 16  (Deposition) - 14 Sep 16  (Release) - 14 Sep 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.93
Chains :  Asym./Biol. Unit :  C,H,L
Keywords :  Fab, Peptide Ligand, Mutation, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Kitago, M. K. Kaneko, S. Ogasawara, Y. Kato, J. Takagi
Structural Basis For Multi-Specific Peptide Recognition By The Anti-Idh1/2 Monoclonal Antibody, Msmab-1.
Biochem. Biophys. Res. Commun. 2016
PubMed-ID: 27553275  |  Reference-DOI: 10.1016/J.BBRC.2016.08.110

(-) Compounds

Molecule 1 - HEAVY CHAIN OF FAB FRAGMENT
    Chains: H
    Engineered: YES
    Expression System: MAMMALIA
    Expression System Cell: HYBRIDOMA
    Expression System Taxid: 40674
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
 
Molecule 2 - LIGHT CHAIN OF FAB FRAGMENT
    Chains: L
    Engineered: YES
    Expression System: MAMMALIA
    Expression System Cell: HYBRIDOMA
    Expression System Taxid: 40674
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
 
Molecule 3 - THR-LYS-PRO-ILE-THR-ILE-GLY-SER-HIS-ALA-HIS-GLY-ASP-GLN- TYR-LYS
    Chains: C
    Engineered: YES
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : CHL

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1PCA1Mod. Amino AcidPYROGLUTAMIC ACID
2SO43Ligand/IonSULFATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER H:161 , GLY H:162 , HOH H:443 , LYS L:169binding site for residue SO4 H 301
2AC2SOFTWAREARG L:108 , HOH L:485binding site for residue SO4 L 301
3AC3SOFTWAREARG H:58 , SER L:93 , TRP L:94binding site for residue SO4 L 302

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1H:22 -H:92
2H:140 -H:195
3L:23 -L:88
4L:134 -L:194

(-) Cis Peptide Bonds  (6, 7)

Asymmetric/Biological Unit
No.Residues
1Phe H:146 -Pro H:147
2Glu H:148 -Pro H:149
3Trp H:188 -Pro H:189
4Ser L:7 -Pro L:8
5Trp L:94 -Pro L:95
6Tyr L:140 -Pro L:141

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5GIS)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5GIS)

(-) Exons   (0, 0)

(no "Exon" information available for 5GIS)

(-) Sequences/Alignments

Asymmetric/Biological 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 C from PDB  Type:PROTEIN  Length:10
                                          
               SCOP domains ---------- SCOP domains
               CATH domains ---------- CATH domains
               Pfam domains ---------- Pfam domains
         Sec.struct. author ....hhhhhh Sec.struct. author
                 SAPs(SNPs) ---------- SAPs(SNPs)
                    PROSITE ---------- PROSITE
                 Transcript ---------- Transcript
                 5gis C 167 PITIGSHAHG 176
                                   176


Chain H from PDB  Type:PROTEIN  Length:211
                                                                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee...eeee.....eeeeeeee..hhhhh.eeeeee.....eeeeeee......eee.hhhh..eeeeeehhh.eeeeee...hhhhheeeeee.........eeeee........eeeee.......eeeeeeeeeee.....eeee.hhh....eee...eee..eeeeeeeeeee.........eeeeeehhhheeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5gis H   1 xVQLQQPGAELVRPGASVKLSCKASGYTFTSYWMNWVKQRPGQGLECIGMIHPSDGETRLNQKFKDKATLTLDKSSSTAYMQLSSPTSEDSAVYYCTTHFDYWGQGTTLTVSSAKTTAPSVYPLAPVCGDSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEPRG 214
                            |       10        20        30        40        50  |     59        69        79   |||  86        96|      110       120       130|      143       153       163       173       183       193       203       213 
                            1-PCA                                             52A                            82A||            96|                          130|                                                                                
                                                                                                              82B|            101                           134                                                                                
                                                                                                               82C                                                                                                                             


Chain L from PDB  Type:PROTEIN  Length:211
                                                                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 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..eee...eeeee.........eeeeeeeeeehhhhh...eeeeeee.......eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5gis L   1 DIVLIQSPATLSVTPGDSVSLSCRASQRISNNLHWYQQKSHESPRLLIRYTSQSISGIPSRFSGSGSGTDFTLSINSVETEDFGMYFCQQSNSWPFTFGSGTKLEMKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR 211
                                    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)
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  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  (0, 0)

(no "SCOP Domain" information available for 5GIS)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5GIS)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5GIS)

(-) Gene Ontology  (19, 19)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
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 Related Entries

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        IDHP_HUMAN | P48735: 4ja8 5i95 5i96 5svn 5svo

(-) Related Entries Specified in the PDB File

5gir