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(-) Description

Title :  CRYSTAL STRUCTURE OF THERAPEUTIC MAB AR20.5 IN COMPLEX WITH MUC1 PEPTIDE
 
Authors :  C. L. Brooks, M. Movahedin
Date :  02 Sep 16  (Deposition) - 11 Jan 17  (Release) - 14 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B,F  (1x)
Biol. Unit 2:  C,D,E  (1x)
Keywords :  Antibody, Fab, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Movahedin, T. M. Brooks, N. T. Supekar, N. Gokanapudi, G. J. Boons, C. L. Brooks
Glycosylation Of Muc1 Influences The Binding Of A Therapeutic Antibody By Altering The Conformational Equilibrium Of The Antigen.
Glycobiology V. 27 677 2017
PubMed-ID: 28025250  |  Reference-DOI: 10.1093/GLYCOB/CWW131

(-) Compounds

Molecule 1 - FAB FRAGMENT AR20.5 - LIGHT CHAIN
    ChainsA, C
    EngineeredYES
    Expression SystemMUS MUSCULUS
    Expression System Cell LineHYBRIDOMA
    Expression System Taxid10090
    FragmentANTIBODY FAB FRAGMENT
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
 
Molecule 2 - FAB FRAGMENT - AR20.5 - HEAVY CHAIN
    ChainsB, D
    EngineeredYES
    Expression SystemMUS MUSCULUS
    Expression System Cell LineHYBRIDOMA
    Expression System Taxid10090
    FragmentMUC1 PEPTIDE APDTRPAP
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
 
Molecule 3 - MUC1 GLYCOPEPTIDE
    ChainsF, E
    EngineeredYES
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SyntheticYES

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit ABCDEF
Biological Unit 1 (1x)AB   F
Biological Unit 2 (1x)  CDE 

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1NGA2Ligand/IonN-ACETYL-D-GALACTOSAMINE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1NGA1Ligand/IonN-ACETYL-D-GALACTOSAMINE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1NGA1Ligand/IonN-ACETYL-D-GALACTOSAMINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG C:193 , TYR D:100 , THR E:4 , PRO E:6binding site for Mono-Saccharide NGA E 101 bound to THR E 4
2AC2SOFTWARETYR B:100 , THR F:4 , PRO F:6binding site for Mono-Saccharide NGA F 101 bound to THR F 4

(-) SS Bonds  (8, 8)

Asymmetric Unit
No.Residues
1A:23 -A:93
2A:139 -A:199
3B:22 -B:96
4B:143 -B:198
5C:23 -C:93
6C:139 -C:199
7D:22 -D:96
8D:143 -D:198

(-) Cis Peptide Bonds  (12, 12)

Asymmetric Unit
No.Residues
1Thr A:7 -Pro A:8
2Val A:99 -Pro A:100
3Tyr A:145 -Pro A:146
4Phe B:149 -Pro B:150
5Glu B:151 -Pro B:152
6Trp B:191 -Pro B:192
7Thr C:7 -Pro C:8
8Val C:99 -Pro C:100
9Tyr C:145 -Pro C:146
10Phe D:149 -Pro D:150
11Glu D:151 -Pro D:152
12Trp D:191 -Pro D:192

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5T78)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5T78)

(-) Exons   (0, 0)

(no "Exon" information available for 5T78)

(-) 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:216
                                                                                                                                                                                                                                                        
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee............eeeeee.....eeeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeeee......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhhh..eeeeeeee..eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5t78 A   1 DVLMTQTPLSLPVSLGDQASISCRSSQTIVHSNGKIYLEWYLQKPGQSPKLLIYRVSKRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGVYYCFQGSHVPWTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR 216
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210      

Chain B from PDB  Type:PROTEIN  Length:209
                                                                                                                                                                                                                                                 
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..eee.....eeeeeeee..hhhhh.eeeeee.....eeeeeee.................eeeee....eeeeee...hhhhheeeeeeee...eeee...eeeee........eeeee....eeeeeeeeeee.....eeee.hhh....eee...eee..eeeeeeeeeee.........eeeeeehhhheeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5t78 B   1 EVKLVESGGGLVAPGGSLKLSCAASGFTFSSYPMSWVRQTPEKRLEWVAYINNGGGNPYYPDTVKGRFTISRDNAKNTLYLQMSSLKSEDTAIYYCIRQYYGFDYWGQGTTLTVSSAKTTPPSVYPLAPNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVP 215
                                    10        20        30        40        50        60        70        80        90       100       110       120       136       146       156       166       176       186       196       206         
                                                                                                                                                          129|                                                                               
                                                                                                                                                           136                                                                               

Chain C from PDB  Type:PROTEIN  Length:216
                                                                                                                                                                                                                                                        
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee............eeeeee.....eeeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeeee......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhhh..eeeeeeee..eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5t78 C   1 DVLMTQTPLSLPVSLGDQASISCRSSQTIVHSNGKIYLEWYLQKPGQSPKLLIYRVSKRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGVYYCFQGSHVPWTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR 216
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210      

Chain D from PDB  Type:PROTEIN  Length:209
                                                                                                                                                                                                                                                 
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..eee.....eeeeeeee..hhhhh.eeeeee.....eeeeeee.................eeeee....eeeeee...hhhhheeeeeeee...eeee...eeeee........eeeee....eeeeeeeeeee.....eeee.hhh....eee...eee..eeeeeeeeeee.........eeeeeehhhheeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5t78 D   1 EVKLVESGGGLVAPGGSLKLSCAASGFTFSSYPMSWVRQTPEKRLEWVAYINNGGGNPYYPDTVKGRFTISRDNAKNTLYLQMSSLKSEDTAIYYCIRQYYGFDYWGQGTTLTVSSAKTTPPSVYPLAPNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVP 215
                                    10        20        30        40        50        60        70        80        90       100       110       120       136       146       156       166       176       186       196       206         
                                                                                                                                                          129|                                                                               
                                                                                                                                                           136                                                                               

Chain E from PDB  Type:PROTEIN  Length:7
                                       
               SCOP domains ------- SCOP domains
               CATH domains ------- CATH domains
               Pfam domains ------- Pfam domains
         Sec.struct. author ....... Sec.struct. author
                 SAPs(SNPs) ------- SAPs(SNPs)
                    PROSITE ------- PROSITE
                 Transcript ------- Transcript
                 5t78 E   2 PDTRPAP   8

Chain F from PDB  Type:PROTEIN  Length:7
                                       
               SCOP domains ------- SCOP domains
               CATH domains ------- CATH domains
               Pfam domains ------- Pfam domains
         Sec.struct. author ....... Sec.struct. author
                 SAPs(SNPs) ------- SAPs(SNPs)
                    PROSITE ------- PROSITE
                 Transcript ------- Transcript
                 5t78 F   2 PDTRPAP   8

   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 5T78)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5T78)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5T78)

(-) Gene Ontology  (26, 26)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        MUC1_HUMAN | P159411sm3 2acm 2fo4 5t6p

(-) Related Entries Specified in the PDB File

5t6p