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(-) Description

Title :  CRYSTAL STRUCTURE OF THE FAB FRAGMENT OF B2212A, A MURINE MONOCLONAL ANTIBODY SPECIFIC FOR THE THIRD FIBRONECTIN DOMAIN (FN3) OF HUMAN ROBO1.
 
Authors :  T. Nakayama, E. Mizohata, T. Yamashita, S. Nagatoishi, M. Nakakido, H. Y. Mochizuki, Y. Kado, Y. Yokota, R. Sato, K. Tsumoto, H. Fujitani, T. K T. Hamakubo, T. Inoue
Date :  12 Sep 13  (Deposition) - 21 Jan 15  (Release) - 04 Mar 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym. Unit :  H,I,L,M
Biol. Unit 1:  H,L  (1x)
Biol. Unit 2:  I,M  (1x)
Keywords :  Immunoglobulin Fab Fragment, Anti-Hepatocellular Carcinoma Antibody, The Third Fibronectin Type-Iii Domain (Fn3) Of Human Robo1, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  T. Nakayama, E. Mizohata, T. Yamashita, S. Nagatoishi, M. Nakakido, H. Iwanari, Y. Mochizuki, Y. Kado, Y. Yokota, R. Satoh, K. Tsumoto, H. Fujitani, T. Kodama, T. Hamakubo, T. Inoue
Structural Features Of Interfacial Tyrosine Residue In Robo Fibronectin Domain-Antibody Complex: Crystallographic, Thermodynamic, And Molecular Dynamic Analyses
Protein Sci. V. 24 328 2015
PubMed-ID: 25492858  |  Reference-DOI: 10.1002/PRO.2619

(-) Compounds

Molecule 1 - ANTI-HUMAN ROBO1 ANTIBODY B2212A FAB LIGHT CHAIN
    ChainsL, M
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
 
Molecule 2 - ANTI-HUMAN ROBO1 ANTIBODY B2212A FAB HEAVY CHAIN
    ChainsH, I
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit HILM
Biological Unit 1 (1x)H L 
Biological Unit 2 (1x) I M

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 3WII)

(-) Sites  (0, 0)

(no "Site" information available for 3WII)

(-) SS Bonds  (8, 8)

Asymmetric Unit
No.Residues
1H:22 -H:96
2H:146 -H:201
3I:22 -I:96
4I:146 -I:201
5L:23 -L:88
6L:134 -L:194
7M:23 -M:88
8M:134 -M:194

(-) Cis Peptide Bonds  (12, 12)

Asymmetric Unit
No.Residues
1Leu L:94 -Pro L:95
2Tyr L:140 -Pro L:141
3Asp H:136 -Thr H:137
4Phe H:152 -Pro H:153
5Glu H:154 -Pro H:155
6Trp H:194 -Pro H:195
7Leu M:94 -Pro M:95
8Tyr M:140 -Pro M:141
9Val I:133 -Cys I:134
10Phe I:152 -Pro I:153
11Glu I:154 -Pro I:155
12Trp I:194 -Pro I:195

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3WII)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3WII)

(-) Exons   (0, 0)

(no "Exon" information available for 3WII)

(-) 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 H from PDB  Type:PROTEIN  Length:220
                                                                                                                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee..hhhhheeeeeeee...eeeeeeee......eee.hhhh..eeeeeehhh.eeeeee...hhhhheeeeeeee........ee...eeeee........eeeee..........eeeeeeeeeee.....eeee.hhh....eee...eee..eeeeeeeeeee.........eeeeeehhh.eeeeee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wii H   1 EVQLQQSGPELVKPGASVKISCKASGYTFTDYYMNWVKLSHGKSLEWIGDIVPNNGDTTYNQNFRGKATLTVDKSSSTAYMELRSLTSEDSAVYYCARFSNYVYPFDYWGQGTTLTVSSAKTTAPSVYPLAPVCGDTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAILQSDLYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEPRA 220
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220

Chain I from PDB  Type:PROTEIN  Length:220
                                                                                                                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee..hhhhheeeeeeee...eeeeeeee......eee.hhhh..eeeeeehhh.eeeeee...hhhhheeeeeeee........ee...eeeee........eeeee..........eeeeeeeeeee.....eeee.hhh....eee...ee....eeeeeeeeee.hhh.....eeeeeehhh.eeeeee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wii I   1 EVQLQQSGPELVKPGASVKISCKASGYTFTDYYMNWVKLSHGKSLEWIGDIVPNNGDTTYNQNFRGKATLTVDKSSSTAYMELRSLTSEDSAVYYCARFSNYVYPFDYWGQGTTLTVSSAKTTAPSVYPLAPVCGDTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAILQSDLYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEPRA 220
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220

Chain L from PDB  Type:PROTEIN  Length:213
                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee....eeee.....eeeeeee.......eeeeee.....eeeeee...ee.......eeeeee..eeeeee...hhhhh.eeeeee......ee...eeeee.......eeeee..hhhhhhhheeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhh...eeeeeee.......eeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wii L   1 DIQMTQTTSSLSASLGDRVTISCRASQDISNFLNWYQQKPDGTVKLLIYYTSRLHSGVPSRFSGSGSGTDFSLTISKLEQEDIATYFCQQGNTLPLTFGAGTKLELKRAEAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNE 213
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210   

Chain M from PDB  Type:PROTEIN  Length:213
                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee....eeee.....eeeeeee.......eeeeee.....eeeeee...ee.......eeeeee..eeeeee...hhhhh.eeeeee......ee...eeeee.......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhh...eeeeeee.......eeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wii M   1 DIQMTQTTSSLSASLGDRVTISCRASQDISNFLNWYQQKPDGTVKLLIYYTSRLHSGVPSRFSGSGSGTDFSLTISKLEQEDIATYFCQQGNTLPLTFGAGTKLELKRAEAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNE 213
                                    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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    → 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 3WII)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3WII)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3WII)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3WII)

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  Cis Peptide Bonds
    Asp H:136 - Thr H:137   [ RasMol ]  
    Glu H:154 - Pro H:155   [ RasMol ]  
    Glu I:154 - Pro I:155   [ RasMol ]  
    Leu L:94 - Pro L:95   [ RasMol ]  
    Leu M:94 - Pro M:95   [ RasMol ]  
    Phe H:152 - Pro H:153   [ RasMol ]  
    Phe I:152 - Pro I:153   [ RasMol ]  
    Trp H:194 - Pro H:195   [ RasMol ]  
    Trp I:194 - Pro I:195   [ RasMol ]  
    Tyr L:140 - Pro L:141   [ RasMol ]  
    Tyr M:140 - Pro M:141   [ RasMol ]  
    Val I:133 - Cys I:134   [ RasMol ]  
 
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(-) Related Entries Specified in the PDB File

3wih CRYSTAL STRUCTURE OF THE THIRD FIBRONECTIN DOMAIN (FN3) OF HUMAN ROBO1 IN COMPLEX WITH THE FAB FRAGMENT OF MURINE MONOCLONAL ANTIBODY B2212A.