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(-) Description

Title :  CRYSTAL STRUCTURE OF FAB 6C8 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) - 21 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  H,L
Keywords :  Immunoglobulin Fold, Mpts Binding, 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 - 6C8 LIGHT CHAIN
    Chains: L
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Other Details: HYBRIDOMA
 
Molecule 2 - 6C8 HEAVY CHAIN
    Chains: H
    Organism Common: MOUSE, MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Other Details: HYBRIDOMA
    Strain: SWISS WEBSTER

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : HL

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 6)

Asymmetric/Biological Unit (4, 6)
No.NameCountTypeFull Name
12M91Ligand/Ion8-METHOXYPYRENE-1,3,6-TRISULFONIC ACID
2ACT2Ligand/IonACETATE ION
3PO41Ligand/IonPHOSPHATE ION
4ZN2Ligand/IonZINC ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU L:27 , GLU L:93 , ASP L:151 , HIS L:189BINDING SITE FOR RESIDUE ZN L 301
2AC2SOFTWAREGLN L:37 , PRO L:59 , ASP L:82BINDING SITE FOR RESIDUE ACT L 302
3AC3SOFTWARELYS L:142BINDING SITE FOR RESIDUE ACT L 303
4AC4SOFTWAREGLY H:97 , TYR H:98 , GLY H:99 , ILE H:100 , ARG H:100A , GLY H:100B , PRO H:200 , SER H:202 , PRO H:225 , HOH H:601 , TYR L:28 , ASN L:30 , PHE L:32 , ARG L:50BINDING SITE FOR RESIDUE 2M9 H 501
5AC5SOFTWARETYR H:100C , ASP H:101 , ASP H:130 , GLU L:55BINDING SITE FOR RESIDUE PO4 H 502
6AC6SOFTWAREHIS H:172 , ASN L:138 , HOH L:438BINDING SITE FOR RESIDUE ZN H 503

(-) 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  (11, 11)

Asymmetric/Biological Unit
No.Residues
1Ser L:7 -Pro L:8
2Asn 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
7Asn H:54 -Gly H:55
8Pro H:126 -Gly H:127
9Phe H:148 -Pro H:149
10Glu H:150 -Pro H:151
11Trp H:199 -Pro H:200

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4NJA)

(-) 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:221
                                                                                                                                                                                                                                                              
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee..hhhhh.eeeeeee...eeeeeeee......eee.hhhh..eeeeee....eeeeee...hhhhheeeeeeee........eeee...eeeee........eeeee..........eeeeeeeeeee.....eeee.hhh.....eeeeeeee..eeeeeeeeeee.hhh.....eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4nja H    1 EVQLQQSGPELVKPGASVKMSCKASGYTFTDYYMHWVKQSHGKSLEWIGYIYPNNGGNGYNQKFKGKATLTVDKSSSTAYMELRSLTSDDSAVYYCARRGGYGIRGYFDVWGTGTTVTVSSAKTTPPSVYPLAPGCGDTTGSSVTSGCLVKGYFPEPVTVTWNSGSLSSSVHTFPALLQSGLYTMSSSVTVPSSTWPSQTVTCSVAHPASSTTVDKKLEPS  226
                                    10        20        30        40        50  |     59        69        79   |||  86        96    |||102       112       122       134       144       154|||    169|      180|      192   || |204 ||    215       225 
                                                                              52A                            82A||               100A|||                           130|                  154|||    169|      180|          196| || 206|                  
                                                                                                              82B|                100B||                            133                   156||     171       183           198 ||  208                  
                                                                                                               82C                 100C|                                                   157|                               200|                       
                                                                                                                                    100D                                                    162                                202                       


Chain L from PDB  Type:PROTEIN  Length:217
                                                                                                                                                                                                                                                          
               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..hhhhhhh.eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhhhh.eeeeeee.......eeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4nja L    1 DIVLTQSPASLAVSLGQRATISCRASESVDSYGNSFMHWYQQKPGQPPKLLIYRASNLESGIPARFSGSGSRTDFTLTINPVEADDVATYYCQQSNEDPRTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNE  213
                                    10        20       27C|       36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       
                                                     27A|||                                                                                                                                                                                          
                                                      27B||                                                                                                                                                                                          
                                                       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 4NJA)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (1, 1)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
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 Related Entries

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

UniProtKB/Swiss-Prot
        KV3A8_MOUSE | P01660: 1ejo 1i8i 1i8k 1j05 1moe 1qfw 2r29 2r69 2r6p 2vl5 3bsz
        Q52L95_MOUSE | Q52L95: 3oz9 4nj9

(-) Related Entries Specified in the PDB File

4nj9 FAB 8B10 IN COMPLEX WITH MPTS