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(-) Description

Title :  DEVELOPMENT OF A THERAPEUTIC MONOCLONAL ANTIBODY TARGETING SECRETED AP2 TO TREAT TYPE 2 DIABETES.
 
Authors :  C. Doyle, G. Birrane
Date :  17 Aug 15  (Deposition) - 13 Jan 16  (Release) - 13 Jan 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym./Biol. Unit :  A,H,L
Keywords :  Ap2, Fabp4, Diabetes, Metabolic Syndrome, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. F. Burak, K. E. Inouye, A. White, A. Lee, G. Tuncman, E. S. Calay, M. Sekiya, A. Tirosh, K. Eguchi, G. Birrane, D. Lightwood, L. Howells, G. Odede, H. Hailu, S. West, R. Garlish, H. Neale, C. Doyle, A. Moore, G. S. Hotamisligil
Development Of A Therapeutic Monoclonal Antibody That Targets Secreted Fatty Acid-Binding Protein Ap2 To Treat Type 2 Diabetes.
Sci Transl Med V. 7 Ra205 2015
PubMed-ID: 26702093  |  Reference-DOI: 10.1126/SCITRANSLMED.AAC6336

(-) Compounds

Molecule 1 - FATTY ACID-BINDING PROTEIN, ADIPOCYTE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: FABP4, AP2
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: 3T3-L1 LIPID-BINDING PROTEIN,ADIPOCYTE LIPID-BINDING PROTEIN,ALBP,ADIPOCYTE-TYPE FATTY ACID-BINDING PROTEIN,AFABP,FATTY ACID-BINDING PROTEIN 4,MYELIN P2 PROTEIN HOMOLOG,P15,P2 ADIPOCYTE PROTEIN,PROTEIN 422
 
Molecule 2 - HA3 FAB HEAVY CHAIN
    Chains: H
    Engineered: YES
    Expression System: CRICETULUS GRISEUS
    Expression System Common: CHINESE HAMSTER
    Expression System Taxid: 10029
    Organism Common: RABBIT
    Organism Scientific: ORYCTOLAGUS CUNICULUS
    Organism Taxid: 9986
 
Molecule 3 - HA3 FAB LIGHT CHAIN
    Chains: L
    Engineered: YES
    Expression System: CRICETULUS GRISEUS
    Expression System Common: CHINESE HAMSTER
    Expression System Taxid: 10029
    Organism Common: RABBIT
    Organism Scientific: ORYCTOLAGUS CUNICULUS
    Organism Taxid: 9986

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : AHL

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1SO41Ligand/IonSULFATE ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:22 , PHE A:28 , ARG A:31 , SER L:93 , HIS L:94 , TYR L:95binding site for residue SO4 A 201

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1H:22 -H:96
2H:146 -H:201
3L:23 -L:89
4L:135 -L:195

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Glu H:154 -Pro H:155
2Trp H:194 -Pro H:195
3Tyr L:95 -Pro L:96
4Tyr L:141 -Pro L:142

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5D8J)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5D8J)

(-) Exons   (0, 0)

(no "Exon" information available for 5D8J)

(-) 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 A from PDB  Type:PROTEIN  Length:133
                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeeeeehhhhhhhhhh.hhhhhhhhh....eeeeeee..eeeeeee....eeeeee.....eeee.....eeeeeeeee..eeeeeeee..eeeeeeeee....eeeeeee..eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5d8j A   0 SMCDAFVGTWKLVSSENFDDYMKEVGVGFATRKVAGMAKPNMIISVNGDLVTIRSESTFKNTEISFKLGVEFDEITADDRKVKSIITLDGGALVQVQKWDGKSTTIKRKRDGDKLVVECVMKGVTSTRVYERA 132
                                     9        19        29        39        49        59        69        79        89        99       109       119       129   


Chain H from PDB  Type:PROTEIN  Length:216
                                                                                                                                                                                                                                                        
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eee...eeee.....eeeeeeee..hhhhh.eeeeee.....eeeeeee......eee.hhhh...eeeee....eeeeee...hhhhheeeeeeeee....eeeee...eeeee........eeeee......eeeeeeeee.......eeee........eee...ee....eeeeeeeeee........eeeeeee....eeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5d8j H   1 QVQLQQPGAELVKPGASVKLSCKASGYTFTSNWITWVKQRPGQGLEWIGDIYPGSGSTTNNEKFKSKATLTVDTSSSTAYMQLSSLTSEDSAVYYCARLRGYYDYFDFWGQGTTLTVSSAKTTPPSVYPLAPGTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPRD 220
                                    10        20        30        40        50        60        70        80        90       100       110       120       130  ||   144       154       164       174       184       194       204       214      
                                                                                                                                                              133|                                                                                  
                                                                                                                                                               138                                                                                  


Chain L from PDB  Type:PROTEIN  Length:214
                                                                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee....hhh.eeeeee......eeee.............eeeeee..eeeeee...hhhhheeeeeee......ee...eeeee.......eeeee..hhhhhhhh..eeeeeeeee.....eeeeee...ee...eeeee.........eeeeeeee.hhhhhh...eeeeeee.......eeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5d8j L   1 EVVLTQSPALMAASPGEKVTITCSVSSSISSSNLHWYQQKSETSPKPWIYGTSNLASGVPVRFSGSGSGTSYSLTISSMEAEDAATYYCQQWSHYPLTFGAGTKLELKRTDAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNE 214
                                    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  (0, 0)

(no "SCOP Domain" information available for 5D8J)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5D8J)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5D8J)

(-) Gene Ontology  (17, 17)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Glu H:154 - Pro H:155   [ RasMol ]  
    Trp H:194 - Pro H:195   [ RasMol ]  
    Tyr L:141 - Pro L:142   [ RasMol ]  
    Tyr L:95 - Pro L:96   [ RasMol ]  
 

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        FABP4_MOUSE | P04117: 1a18 1a2d 1ab0 1acd 1adl 1alb 1g74 1g7n 1lib 1lic 1lid 1lie 1lif 2ans 2q9s 2qm9 3hk1 3js1 3jsq 5c0n

(-) Related Entries Specified in the PDB File

5c0n 5C0N CONTAINS THE SAME PROTEIN COMPLEXED WITH THE FAB OF CA33 ANTIBODY