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(-) Description

Title :  STRUCTURE OF IGG1 FAB FRAGMENT IN COMPLEX WITH BIOTINCYTIDINAMIDE
 
Authors :  S. Dengl, E. Hoffmann, M. Grote, C. Wagner, O. Mundigl, G. Georges, I. Th G. Stubenrauch, A. Bujotzek, H. -P. Josel, S. Dziadek, J. Benz, U. Brin
Date :  13 Jan 15  (Deposition) - 04 Mar 15  (Release) - 13 May 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  C,D,E,F,H,L,O,P
Biol. Unit 1:  H,L  (1x)
Biol. Unit 2:  C,D  (1x)
Biol. Unit 3:  E,F  (1x)
Biol. Unit 4:  O,P  (1x)
Keywords :  Antibody, Fab Fragment, Hapten, Mab_m33_fab_fragment, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Dengl, E. Hoffmann, M. Grote, C. Wagner, O. Mundigl, G. Georges, I. Thorey, K. G. Stubenrauch, A. Bujotzek, H. P. Josel, S. Dziadek, J. Benz, U. Brinkmann
Hapten-Directed Spontaneous Disulfide Shuffling: A Universa Technology For Site-Directed Covalent Coupling Of Payloads To Antibodies.
Faseb J. V. 29 1763 2015
PubMed-ID: 25670234  |  Reference-DOI: 10.1096/FJ.14-263665

(-) Compounds

Molecule 1 - MAB M33 FAB FRAGMENT, HEAVY CHAIN
    Chains: H, C, E, O
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
 
Molecule 2 - MAB M33 FAB FRAGMENT, LIGHT CHAIN
    Chains: L, D, F, P
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : CDEFHLOP
Biological Unit 1 (1x):     HL  
Biological Unit 2 (1x): CD      
Biological Unit 3 (1x):   EF    
Biological Unit 4 (1x):       OP

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric Unit (2, 5)
No.NameCountTypeFull Name
141M4Ligand/IonN~6~-{5-[(3AS,4S,6AR)-2-OXOHEXAHYDRO-1H-THIENO[3,4-D]IMIDAZOL-4-YL]PENTANOYL}-L-LYSINAMIDE
2SO41Ligand/IonSULFATE ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
141M1Ligand/IonN~6~-{5-[(3AS,4S,6AR)-2-OXOHEXAHYDRO-1H-THIENO[3,4-D]IMIDAZOL-4-YL]PENTANOYL}-L-LYSINAMIDE
2SO4-1Ligand/IonSULFATE ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
141M1Ligand/IonN~6~-{5-[(3AS,4S,6AR)-2-OXOHEXAHYDRO-1H-THIENO[3,4-D]IMIDAZOL-4-YL]PENTANOYL}-L-LYSINAMIDE
2SO4-1Ligand/IonSULFATE ION
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
141M1Ligand/IonN~6~-{5-[(3AS,4S,6AR)-2-OXOHEXAHYDRO-1H-THIENO[3,4-D]IMIDAZOL-4-YL]PENTANOYL}-L-LYSINAMIDE
2SO4-1Ligand/IonSULFATE ION
Biological Unit 4 (2, 2)
No.NameCountTypeFull Name
141M1Ligand/IonN~6~-{5-[(3AS,4S,6AR)-2-OXOHEXAHYDRO-1H-THIENO[3,4-D]IMIDAZOL-4-YL]PENTANOYL}-L-LYSINAMIDE
2SO41Ligand/IonSULFATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN H:29 , ASP H:31 , THR H:32 , PHE H:33 , TRP H:99 , HOH H:451 , LEU L:33 , SER L:34 , SER L:50 , PHE L:91BINDING SITE FOR RESIDUE 41M H 301
2AC2SOFTWAREASN C:29 , ASP C:31 , THR C:32 , PHE C:33 , TRP C:99 , TRP C:106 , HOH C:344 , TYR D:32 , LEU D:33 , SER D:34 , SER D:50 , PHE D:91 , TYR D:96BINDING SITE FOR RESIDUE 41M D 301
3AC3SOFTWAREASN E:29 , THR E:32 , PHE E:33 , TRP E:99 , TRP E:106 , TYR F:32 , LEU F:33 , SER F:34 , SER F:50 , PHE F:91BINDING SITE FOR RESIDUE 41M E 301
4AC4SOFTWARELYS H:59 , SER O:24 , SER O:25 , GLY O:26 , LYS O:30 , ASN O:77 , HOH O:402 , HOH O:406 , HOH O:423BINDING SITE FOR RESIDUE SO4 O 301
5AC5SOFTWAREASN O:29 , ASP O:31 , PHE O:33 , TRP O:99 , TRP O:106 , LEU P:33 , SER P:34 , SER P:50 , PHE P:91 , TYR P:96 , HOH P:443BINDING SITE FOR RESIDUE 41M P 301

(-) SS Bonds  (16, 16)

Asymmetric Unit
No.Residues
1C:96 -C:22
2C:202 -C:147
3D:88 -D:23
4D:194 -D:134
5E:96 -E:22
6E:202 -E:147
7F:88 -F:23
8F:194 -F:134
9H:22 -H:96
10H:147 -H:202
11L:23 -L:88
12L:134 -L:194
13O:96 -O:22
14O:202 -O:147
15P:88 -P:23
16P:194 -P:134

(-) Cis Peptide Bonds  (20, 20)

Asymmetric Unit
No.Residues
1Phe H:153 -Pro H:154
2Glu H:155 -Pro H:156
3Trp H:195 -Pro H:196
4Ser L:7 -Pro L:8
5Tyr L:140 -Pro L:141
6Phe C:153 -Pro C:154
7Glu C:155 -Pro C:156
8Trp C:195 -Pro C:196
9Ser D:7 -Pro D:8
10Tyr D:140 -Pro D:141
11Phe E:153 -Pro E:154
12Glu E:155 -Pro E:156
13Trp E:195 -Pro E:196
14Ser F:7 -Pro F:8
15Tyr F:140 -Pro F:141
16Phe O:153 -Pro O:154
17Glu O:155 -Pro O:156
18Trp O:195 -Pro O:196
19Ser P:7 -Pro P:8
20Tyr P:140 -Pro P:141

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4S1D)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4S1D)

(-) Exons   (0, 0)

(no "Exon" information available for 4S1D)

(-) 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 C from PDB  Type:PROTEIN  Length:212
                                                                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee...eee.....eeeeeeee........eeeeee.....eeeeeee......eee.hhhh..eeeeee....eeeeee...hhhhheeeeeeeeeee..eeeeee...eeeee........eeeee...eeeeeeeeeee.....eeee.hhh.....ee...eee..eeeeeeeeeee.........eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4s1d C   2 VQLQQSGAELVKPGASVKLSCTSSGFNNKDTFFQWVKQRPEEGLEWIGRIDPANGFTKYDPKFQGKATITVDTSSNTAYLQLNSLTSEDTALYYCTRWDTYGAAWFAYWGQGTLVTVSAAKTTPPSVYPLAPSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPR 220
                                    11        21        31        41        51        61        71        81        91       101       111       121       131 ||    148       158       168       178       188       198       208       218  
                                                                                                                                                             133|                                                                               
                                                                                                                                                              141                                                                               


Chain D from PDB  Type:PROTEIN  Length:211
                                                                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee...........eeeeee......eeeee..hhhhhhhheeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhhh...eeeeee.........eee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4s1d D   1 DIQMTQSPASLSASVGETVTITCRASGNIHNYLSWFQQKQGKSPQLLVYSAKTLADGVPSRFSGSGSGTQYSLKINSLQPEDFGTYYCQHFWSSIYTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR 211
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210 


Chain E from PDB  Type:PROTEIN  Length:214
                                                                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee........eeeeee......eeeeee......eee.hhhh..eeeeeehhh.eeeeee...hhhhheeeeeeeeeee..eeeeee...eeeee........eeeee.....eeeeeeeeeee.....eeee........eee...ee....eeeeeeeeee.........eeeeee....eeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4s1d E   1 EVQLQQSGAELVKPGASVKLSCTSSGFNNKDTFFQWVKQRPEEGLEWIGRIDPANGFTKYDPKFQGKATITVDTSSNTAYLQLNSLTSEDTALYYCTRWDTYGAAWFAYWGQGTLVTVSAAKTTPPSVYPLAPGNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVP 219
                                    10        20        30        40        50        60        70        80        90       100       110       120       130   ||  145       155       165       175       185       195       205       215    
                                                                                                                                                               134|                                                                               
                                                                                                                                                                140                                                                               


Chain F from PDB  Type:PROTEIN  Length:213
                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee...........eeeeee......eeeee..hhhhhhhheeeeeeeeeee.....eeeeee..eee.....eee.........eeeeeeeeeehhhhhhh..eeeeee.......eee...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4s1d F   1 DIQMTQSPASLSASVGETVTITCRASGNIHNYLSWFQQKQGKSPQLLVYSAKTLADGVPSRFSGSGSGTQYSLKINSLQPEDFGTYYCQHFWSSIYTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNE 213
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210   


Chain H from PDB  Type:PROTEIN  Length:216
                                                                                                                                                                                                                                                        
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee........eeeeee......eeeeee......eee.hhhh..eeeeee....eeeeee...hhhhheeeeeeeeeee..eeeeee...eeeee........eeeee......eeeeeeeeeee.....eeee.hhh....eee...ee....eeeeeeeeee.........eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4s1d H   1 EVQLQQSGAELVKPGASVKLSCTSSGFNNKDTFFQWVKQRPEEGLEWIGRIDPANGFTKYDPKFQGKATITVDTSSNTAYLQLNSLTSEDTALYYCTRWDTYGAAWFAYWGQGTLVTVSAAKTTPPSVYPLAPGSNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPR 220
                                    10        20        30        40        50        60        70        80        90       100       110       120       130    || 144       154       164       174       184       194       204       214      
                                                                                                                                                                135|                                                                                
                                                                                                                                                                 140                                                                                


Chain L from PDB  Type:PROTEIN  Length:213
                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee.......eeeeee.....eeeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee...........eeeee.......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhh...eeeeeeee..eeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4s1d L   1 DIQMTQSPASLSASVGETVTITCRASGNIHNYLSWFQQKQGKSPQLLVYSAKTLADGVPSRFSGSGSGTQYSLKINSLQPEDFGTYYCQHFWSSIYTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNE 213
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210   


Chain O from PDB  Type:PROTEIN  Length:213
                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee........eeeeee.....eeeeeee......eee.......eeeeeehhh.eeeeee...hhhhheeeeeeeeeee..eeeeee...eeeee........eeeee...eeeeeeeeeee.....eeee........eee...eee..eeeeeeeeeee.........eeeeee....eeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4s1d O   1 EVQLQQSGAELVKPGASVKLSCTSSGFNNKDTFFQWVKQRPEEGLEWIGRIDPANGFTKYDPKFQGKATITVDTSSNTAYLQLNSLTSEDTALYYCTRWDTYGAAWFAYWGQGTLVTVSAAKTTPPSVYPLAPSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPR 220
                                    10        20        30        40        50        60        70        80        90       100       110       120       130  ||   147       157       167       177       187       197       207       217   
                                                                                                                                                              133|                                                                               
                                                                                                                                                               141                                                                               


Chain P from PDB  Type:PROTEIN  Length:210
                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee...........eeeee.......eeeee..hhhhhhh..eeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeehhhhhhh...eeeeee.......eeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4s1d P   1 DIQMTQSPASLSASVGETVTITCRASGNIHNYLSWFQQKQGKSPQLLVYSAKTLADGVPSRFSGSGSGTQYSLKINSLQPEDFGTYYCQHFWSSIYTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFN 210
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210
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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 4S1D)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4S1D)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4S1D)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
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  4s1d
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