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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 :  01 Sep 16  (Deposition) - 11 Jan 17  (Release) - 14 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.97
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
    Chains: A, C
    Engineered: YES
    Expression System: MUS MUSCULUS
    Expression System Cell Line: HYBRIDOMA, AR20.5
    Expression System Taxid: 10090
    Fragment: ANTIBODY FAB FRAGMENT
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
 
Molecule 2 - FAB FRAGMENT - HEAVY CHAIN
    Chains: B, D
    Engineered: YES
    Expression System: MUS MUSCULUS
    Expression System Cell Line: HYBRIDOMA AR20.5
    Expression System Taxid: 10090
    Fragment: MUC1 PEPTIDE APDTRPAP
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
 
Molecule 3 - MUC1 PEPTIDE FRAGMENT
    Chains: E, F
    Engineered: YES
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synthetic: YES

 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  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 5T6P)

(-) Sites  (0, 0)

(no "Site" information available for 5T6P)

(-) 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 5T6P)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5T6P)

(-) Exons   (0, 0)

(no "Exon" information available for 5T6P)

(-) 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......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
                 5t6p 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:206
                                                                                                                                                                                                                                              
               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...eeeeeeeeee.....eeee.hhh....eee...eee..eeeeeeeeee..........eeeeee....eeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5t6p B   2 VKLVESGGGLVAPGGSLKLSCAASGFTFSSYPMSWVRQTPEKRLEWVAYINNGGGNPYYPDTVKGRFTISRDNAKNTLYLQMSSLKSEDTAIYYCIRQYYGFDYWGQGTTLTVSSAKTTPPSVYPLAPMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVP 215
                                    11        21        31        41        51        61        71        81        91       101       111       121       139       149       159       169       179       189       199       209      
                                                                                                                                                         129|                                                                             
                                                                                                                                                          138                                                                             


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..hhhhhhhheeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhh...eeeeeeee..eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5t6p 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:206
                                                                                                                                                                                                                                              
               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...eeeeeeeeee.....eeee.hhh....eee...eee..eeeeeeeeee..........eeeeee....eeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5t6p D   2 VKLVESGGGLVAPGGSLKLSCAASGFTFSSYPMSWVRQTPEKRLEWVAYINNGGGNPYYPDTVKGRFTISRDNAKNTLYLQMSSLKSEDTAIYYCIRQYYGFDYWGQGTTLTVSSAKTTPPSVYPLAPMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVP 215
                                    11        21        31        41        51        61        71        81        91       101       111       121       139       149       159       169       179       189       199       209      
                                                                                                                                                         129|                                                                             
                                                                                                                                                          138                                                                             


Chain E from PDB  Type:PROTEIN  Length:6
                                      
               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
                 5t6p E   3 DTRPAP   8


Chain F from PDB  Type:PROTEIN  Length:6
                                      
               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
                 5t6p F   3 DTRPAP   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 5T6P)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5T6P)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5T6P)

(-) Gene Ontology  (26, 26)

Asymmetric Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Glu B:151 - Pro B:152   [ RasMol ]  
    Glu D:151 - Pro D:152   [ RasMol ]  
    Phe B:149 - Pro B:150   [ RasMol ]  
    Phe D:149 - Pro D:150   [ RasMol ]  
    Thr A:7 - Pro A:8   [ RasMol ]  
    Thr C:7 - Pro C:8   [ RasMol ]  
    Trp B:191 - Pro B:192   [ RasMol ]  
    Trp D:191 - Pro D:192   [ RasMol ]  
    Tyr A:145 - Pro A:146   [ RasMol ]  
    Tyr C:145 - Pro C:146   [ RasMol ]  
    Val A:99 - Pro A:100   [ RasMol ]  
    Val C:99 - Pro C:100   [ RasMol ]  
 
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        MUC1_HUMAN | P15941: 1sm3 2acm 2fo4 5t78

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