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(-) Description

Title :  CRYSTAL STRUCTURE OF FAB 8B10 IN COMPLEX WITH MPTS
 
Authors :  R. L. Stanfield, F. E. Romesberg, J. Zimmermann, I. A. Wilson
Date :  08 Nov 13  (Deposition) - 12 Nov 14  (Release) - 14 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym./Biol. Unit :  H,L
Keywords :  Immunoglobulin Fold, Mpts, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Adhikary, W. Yu, M. Oda, R. C. Walker, T. Chen, R. L. Stanfield, I. A. Wilson, J. Zimmermann, F. E. Romesberg
Adaptive Mutations Alter Antibody Structure And Dynamics During Affinity Maturation.
Biochemistry V. 54 2085 2015
PubMed-ID: 25756188  |  Reference-DOI: 10.1021/BI501417Q

(-) Compounds

Molecule 1 - 8B10 LIGHT CHAIN
    Chains: L
    Organism Common: MOUSE, MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Other Details: HYBRIDOMA CELLS
    Strain: SWISS WEBSTER
 
Molecule 2 - 8B10 HEAVY CHAIN
    Chains: H
    Organism Common: MOUSE, MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Other Details: HYBRIDOMA CELLS
    Strain: SWISS WEBSTER

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : HL

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 7)

Asymmetric/Biological Unit (2, 7)
No.NameCountTypeFull Name
12M91Ligand/Ion8-METHOXYPYRENE-1,3,6-TRISULFONIC ACID
2ZN6Ligand/IonZINC ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU L:185 , HIS L:189 , HOH L:532 , HOH L:533 , HOH L:534BINDING SITE FOR RESIDUE ZN L 301
2AC2SOFTWAREGLU H:1 , GLU L:27 , GLU L:93BINDING SITE FOR RESIDUE ZN L 302
3AC3SOFTWARELYS L:149 , GLU L:195 , GLU L:213BINDING SITE FOR RESIDUE ZN L 303
4AC4SOFTWAREGLU H:1 , ASP L:1 , HOH L:535BINDING SITE FOR RESIDUE ZN L 304
5AC5SOFTWAREASP L:151 , HIS L:189BINDING SITE FOR RESIDUE ZN L 305
6AC6SOFTWAREGLY H:97 , TYR H:98 , GLY H:99 , SER H:100 , ARG H:100A , GLY H:100B , HOH H:607 , HOH H:673 , GLY L:16 , GLN L:17 , TYR L:28 , ILE L:30 , ARG L:50 , ILE L:76 , PRO L:77 , HOH L:401BINDING SITE FOR RESIDUE 2M9 H 501
7AC7SOFTWAREHIS H:172 , HOH H:708 , ASN L:138 , HOH L:530BINDING SITE FOR RESIDUE ZN H 502

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1H:22 -H:92
2H:142 -H:208
3L:23 -L:88
4L:134 -L:194

(-) Cis Peptide Bonds  (9, 9)

Asymmetric/Biological Unit
No.Residues
1Ser L:7 -Pro L:8
2Ile L:76 -Pro L:77
3Asp L:94 -Pro L:95
4Tyr L:140 -Pro L:141
5Gln L:156 -Asn L:157
6His H:41 -Gly H:42
7Phe H:148 -Pro H:149
8Glu H:150 -Pro H:151
9Trp H:199 -Pro H:200

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4NJ9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4NJ9)

(-) Exons   (0, 0)

(no "Exon" information available for 4NJ9)

(-) 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 H from PDB  Type:PROTEIN  Length:217
                                                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee..hhhhh.eeeeee.....eeeeeee......eee.hhhh..eeeeeehhh.eeeeee...hhhhheeeeeeee........eeee...eeeee........eeeee.....eeeeeeeeeee.....eeee.hhh....eee...eee..eeeeeeeeeee.........eeeeeehhhheeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4nj9 H    1 EVQLQQSGPELVKPGTSVKMSCKASGYTFTDYYMHWVKQSHGKSLEWIGYIYPNNGGNGYNQKFKGKATLTVDKSSSTAYMELRSLTSEDSAVYYCARRGGYGSRGYFDVWGTGTTVTVSSAKTTAPSVYPLAPVGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPALLQSGLYTLSSSVTVTSNTWPSQTITCNVAHPASSTKVDKKIEPRG  227
                                    10        20        30        40        50  |     59        69        79   |||  86        96    |||102       112       122    || 139       149    |||164    || 175    || 187       198 ||   |210       220       
                                                                              52A                            82A||               100A|||                        127|                154|||    169|      180|          196| || 206|                   
                                                                                                              82B|                100B||                         135                 156||     171       183           198 ||  208                   
                                                                                                               82C                 100C|                                              157|                               200|                        
                                                                                                                                    100D                                               162                                202                        


Chain L from PDB  Type:PROTEIN  Length:212
                                                                                                                                                                                                                                                     
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee....ee..ee.eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeeee......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhh...eeeeeee..eeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4nj9 L    1 DIVLTQSPASLAVSLGQRATISCRASESVDSYGISFMHWYQQKPGQPPKLLIYRASNLESGIPARFSGSGSRTDFTLTIIPVEADDVATYYCQQSNEDPRTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATSPIVKSFNRNE  213
                                    10        20       27C|       36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196||     211  
                                                     27A|||                                                                                                                                                                       197|          
                                                      27B||                                                                                                                                                                        203          
                                                       27C|                                                                                                                                                                                     
                                                        27D
   Legend:   → Mismatch (orange background)
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  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 4NJ9)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4NJ9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4NJ9)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 4NJ9)

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  Cis Peptide Bonds
    Asp L:94 - Pro L:95   [ RasMol ]  
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    Ser L:7 - Pro L:8   [ RasMol ]  
    Trp H:199 - Pro H:200   [ RasMol ]  
    Tyr L:140 - Pro L:141   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        Q52L95_MOUSE | Q52L95: 3oz9 4nja
UniProtKB/TrEMBL
        Q9D8L4_MOUSE | Q9D8L4: 1f11

(-) Related Entries Specified in the PDB File

4nja