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(-) Description

Title :  CRYSTAL STRUCTURE OF ANTI-GP41 FAB NC-1
 
Authors :  R. L. Stanfield, D. A. Calarese, S. Jiang, I. A. Wilson
Date :  24 Sep 10  (Deposition) - 06 Oct 10  (Release) - 28 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  H,L
Keywords :  Immunoglobulin Fold, Non-Neutralizing Antibody, Hiv-1 Gp41 6-Helix Bundle Core, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. L. Stanfield, D. A. Calarese, S. Jiang, I. A. Wilson
Crystal Structure Of Anti-Gp41 Fab Nc-1
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - FAB NC-1 KAPPA LIGHT CHAIN
    Chains: L
    Organism Common: MOUSE, MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Other Details: HYBRIDOMA
 
Molecule 2 - FAB NC-1 IGG2A HEAVY CHAIN
    Chains: H
    Organism Common: MOUSE, MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Other Details: HYBRIDOMA
    Synonym: IMMUNOGLOBULIN HEAVY CHAIN GAMMA POLYPEPTIDE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : HL

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1GOL4Ligand/IonGLYCEROL

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR H:96 , TRP H:100A , TYR L:49 , ALA L:55 , SER L:56 , HOH L:382BINDING SITE FOR RESIDUE GOL L 214
2AC2SOFTWAREGLY L:66 , SER L:67BINDING SITE FOR RESIDUE GOL L 215
3AC3SOFTWAREGLU H:150 , PRO H:151 , VAL H:152 , ALA H:176 , LEU H:187 , HOH H:413BINDING SITE FOR RESIDUE GOL H 229
4AC4SOFTWAREPRO H:99 , THR H:100 , SER L:31 , HIS L:34 , TRP L:91 , HOH L:217 , HOH L:282 , HOH L:462BINDING SITE FOR RESIDUE GOL H 230

(-) 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  (5, 5)

Asymmetric/Biological Unit
No.Residues
1Ser L:7 -Pro L:8
2Tyr L:140 -Pro L:141
3Phe H:148 -Pro H:149
4Glu H:150 -Pro H:151
5Trp H:199 -Pro H:200

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3OZ9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3OZ9)

(-) Exons   (0, 0)

(no "Exon" information available for 3OZ9)

(-) 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:219
 aligned with Q569W9_MOUSE | Q569W9 from UniProtKB/TrEMBL  Length:468

    Alignment length:221
                                                                                                                                    124                                                                                                                  
                                                                                                                                 123  |                                                                                                                  
                                    29        39        49        59        69        79        89        99       109       119   |  |127       137       147       157       167       177       187       197       207       217       227       237 
        Q569W9_MOUSE     20 EVQLQQSGAELVRPGSSVKLSCKTSGYTFTSYYINWVKQRPGQGLEWIGHIYPGNGYTEYNEKFKGKATLTSDTSSSTAYMQLRSLTSENSAIYFCARTGGYDG--YFDYWGQGTTITVSSAKTTAPSVYPLAPVCGDTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEPR  238
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -V-set-3oz9H02 H:2-111                                                                                                 --------------C1-set-3oz9H01 H:126-220                                                          ------ Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee..hhhhh.eeeeee.....eeeeeee......eee.hhhh..eeeeee....eeeeee...hhhhheeeeeee--.........ee...eeeee........eeeee..........eeeeeeeeeee.....eeee.hhh....eeeeeeeee..eeeeeeeeeee.........eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3oz9 H    1 QVQLQQSGTELMKPGSSVKISCKATGYRFSSYWVEWVKQRPGHGLEWIGKILPGIGSTSYNEKFKGKATFTADTSSNTAYMQLSSLTSEDSAVYYCAR--GYYGPTWFAYWGQGTLVTVSSAKTTAPSVYPLAPVCGDTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEPR  228
                                    10        20        30        40        50  |     59        69        79   |||  86       | -|     |102       112       122       134       144       154|||    169|      180|      192   || |204 ||    215       227 
                                                                              52A                            82A||          94 95  100A|                           130|                  154|||    169|      180|          196| || 206|            223|  
                                                                                                              82B|                  100B                            133                   156||     171       183           198 ||  208             226  
                                                                                                               82C                                                                         157|                               200|                       
                                                                                                                                                                                            162                                202                       


Chain L from PDB  Type:PROTEIN  Length:211
 aligned with Q52L95_MOUSE | Q52L95 from UniProtKB/TrEMBL  Length:236

    Alignment length:213
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232   
        Q52L95_MOUSE     23 DIKMTQSPSSMYVSLGEAVTITCKASQDIYSFLKWFQKKPGKPPKTLIYHTDRLMDGVPSRFSGSGSGQDYSLTINSLECEDMGIYYCLQYDEFPLTFGGGTKLELRRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNE  235
               SCOP domains d3oz9l1 L:1-110 automated m atches                                                                            d3oz9l2 L:111-213 automated matches                                                                     SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains V-set-3oz9L02 L:1-106                                                                                     ------------C1-set-3oz9L01 L:119-206                                                                ------- Pfam domains
         Sec.struct. author ...ee....eeee.....eeeeeee..-.....eeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeeee...-eee...eeeee.......eeeee..hhhhhhh.eeeeeeeeeee....eeeeeee..eee...eeeee.........eeeeeeeeeehhhhhh..eeeeeeee..eeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3oz9 L    1 QIVLTQSPVIMSASLGEEITLTCSASS-SVSYMHWYQQKSGTSPKLLIYSTSNLASGVPSRFSGSGSGTFYSLTISSVEAEDAADYYCHQWSGF-YTFGGGTKLEIQRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNE  213
                                    10        20      | 30        40        50        60        70        80        90   | | 100       110       120       130       140       150       160       170       180       190       200       210   
                                                     27 |                                                               94 |                                                                                                                     
                                                       29                                                                 96                                                                                                                     


Chain L from PDB  Type:PROTEIN  Length:211
 aligned with Q5XFY8_MOUSE | Q5XFY8 from UniProtKB/TrEMBL  Length:235

    Alignment length:212
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232  
        Q5XFY8_MOUSE     23 QIVLSQSPAILSGFPGEKVTMTCRASSSVNYMHWYQQKPGSSPKPWIYATSKLASGVPARFSGSGSGTSYSLTISRVEAEDAATYYCQQWSSNPLTFGAGTRLELKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNE  234
               SCOP domains d3oz9l1 L:1-110 automated matches                                                                            d3oz9l2 L:111-213 automated matches                                                                     SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains V-set-3oz9L02 L:1-106                                                                                    ------------C1-set-3oz9L01 L:119-206                                                                ------- Pfam domains
         Sec.struct. author ...ee....eeee.....eeeeeee.......eeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeeee...-eee...eeeee.......eeeee..hhhhhhh.eeeeeeeeeee....eeeeeee..eee...eeeee.........eeeeeeeeeehhhhhh..eeeeeeee..eeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3oz9 L    1 QIVLTQSPVIMSASLGEEITLTCSASSSVSYMHWYQQKSGTSPKLLIYSTSNLASGVPSRFSGSGSGTFYSLTISSVEAEDAADYYCHQWSGF-YTFGGGTKLEIQRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNE  213
                                    10        20      ||31        41        51        61        71        81        91  | |  101       111       121       131       141       151       161       171       181       191       201       211  
                                                     27|                                                               94 |                                                                                                                     
                                                      29                                                                 96
   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  (2, 2)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3OZ9)

(-) Pfam Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Clan: Ig (577)

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)
Chain H   (Q569W9_MOUSE | Q569W9)

Chain L   (Q5XFY8_MOUSE | Q5XFY8)

Chain L   (Q52L95_MOUSE | Q52L95)

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 Related Entries

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

UniProtKB/Swiss-Prot
        GCAA_MOUSE | P01863: 1dqm 1dqq 1ehl 1fe8 1ggi 1igt 1keg 1kn2 1kn4 1kno 1mh5 1mnu 1mpa 1ob1 1pg7 1uyw 1yec 1yef 1yeg 1yeh 1yei 1yej 1yek 2ipu 2mpa 2r0w 2r0z 2r29 2r69 2r6p 2vl5 2zch 2zck 2zcl 3bgf 3zo0 4f37 5vaa
        Q52L95_MOUSE | Q52L95: 4nj9 4nja
UniProtKB/TrEMBL
        Q569W9_MOUSE | Q569W9: 1nbz 1ruq 1rur
        Q5XFY8_MOUSE | Q5XFY8: 2j4w 2j5l

(-) Related Entries Specified in the PDB File

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