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(-) Description

Title :  CRYSTAL STRUCTURE OF GP41 DERIVED PROTEIN COMPLEXED WITH FAB 8066
 
Authors :  M. Li, E. Gustchina, J. Louis, A. Gustchina, A. Wlodawer, M. Clore
Date :  23 Mar 10  (Deposition) - 01 Dec 10  (Release) - 01 Dec 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.05
Chains :  Asym./Biol. Unit :  A,H,L
Keywords :  Gp41, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Gustchina, M. Li, J. M. Louis, D. E. Anderson, J. Lloyd, C. Frisch, C. A. Bewley, A. Gustchina, A. Wlodawer, G. M. Clore
Structural Basis Of Hiv-1 Neutralization By Affinity Mature Fabs Directed Against The Internal Trimeric Coiled-Coil Of Gp41.
Plos Pathog. V. 6 E1001 2010
PubMed-ID: 21085615  |  Reference-DOI: 10.1371/JOURNAL.PPAT.1001182

(-) Compounds

Molecule 1 - TRANSMEMBRANE GLYCOPROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: HUMAN IMMUNODEFICIENCY VIRUS 1
    Organism Taxid: 11676
    Synonym: GP41
 
Molecule 2 - FAB8066 FAB ANTIBODY FRAGMENT, HEAVY CHAIN
    Chains: H
    Engineered: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 3 - FAB8066 FAB ANTIBODY FRAGMENT, LIGHT CHAIN
    Chains: L
    Engineered: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : AHL

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1NA2Ligand/IonSODIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETRP A:30 , SER H:50 , ASN H:58 , TRP L:90 , VAL L:95BINDING SITE FOR RESIDUE NA H 245
2AC2SOFTWARESER H:74 , SER H:76 , GLY L:24 , ASN L:26 , ASN L:68BINDING SITE FOR RESIDUE NA L 214

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1H:22 -H:95
2H:147 -H:203
3L:22 -L:87
4L:136 -L:195

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Phe H:153 -Pro H:154
2Glu H:155 -Pro H:156
3Ile L:27 -Pro L:28
4Tyr L:142 -Pro L:143

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3MA9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3MA9)

(-) Exons   (0, 0)

(no "Exon" information available for 3MA9)

(-) 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 A from PDB  Type:PROTEIN  Length:197
 aligned with D0VWW0_9HIV1 | D0VWW0 from UniProtKB/TrEMBL  Length:226

    Alignment length:216
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210      
         D0VWW0_9HIV1     1 MQLLSGIVQQQNNLLRAIEAQQHLLQLTVWGIKQLQARILAGGSGGHTTWMEWDREINNYTSLIHSLIEESQNQQEKNEQELLEGSSGGQLLSGIVQQQNNLLRAIEAQQHLLQLTVWGIKQLQARILAGGSGGHTTWMEWDREINNYTSLIHSLIEESQNQQEKNEQELLEGSSGGQLLSGIVQQQNNLLRAIEAQQHLLQLTVWGIKQLQARIL 216
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..----hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh----hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...-------.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh----hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3ma9 A   1 MQLLSGIVQQQNNLLRAIEAQQHLLQLTVWGIKQLQARILAG----HTTWMEWDREINNYTSLIHSLIEESQNQQEKNEQELLE----GQLLSGIVQQQNNLLRAIEAQQHLLQLTVWGIKQLQARIL-------TTWMEWDREINNYTSLIHSLIEESQNQQEKNEQELLE----GQLLSGIVQQQNNLLRAIEAQQHLLQLTVWGIKQLQARIL 216
                                    10        20        30        40 |    | 50        60        70        80   |    90       100       110       120       | -     | 140       150       160       170 |    |180       190       200       210      
                                                                    42   47                                   84   89                                    128     136                                 172  177                                       


Chain H from PDB  Type:PROTEIN  Length:214
                                                                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee...eee.....eeeeeee...hhhhh.eeeeee......eeeeee......eee.hhhh..eeeeee....eeeeee...hhhhheeeeeee...........ee...eeeee........eeeee.....eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhh.....eeeeeehhhheeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ma9 H   3 QLVQSGAEVKKPGSSVKVSCKASGGTFNSYAFSWVRQAPGQGLEWMGSIIPIFGTTNYAQKFQGRVTITADESTSTAYMELSSLRSEDTAVYYCARYFDTYNNYGFANWGQGTLVTVSSASTKGPSVFPLAPSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEP 220
                                    12        22        32        42        52|       61        71        81        91       101       111       121       131  ||   146       156       166       176       186       196       206       216    
                                                                            52A                                                                               134|                                                                                
                                                                                                                                                               140                                                                                


Chain L from PDB  Type:PROTEIN  Length:209
                                                                                                                                                                                                                                                 
               SCOP domains d3ma9l1 L:2-109 automated matches                                                                           d3ma9l2 L:110-210 automated matches                                                                   SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeee.....eeeeee....hhhh.eeeee......eeeee............eeeeee..eeeeee...hhhhheeeeeeee......eee...eeeee........eeeee..hhhhhhh..eeeeeeeeee.....eeeeee..eee...eee...ee.....eeeeeeeeehhhhhhh...eeeeeee..eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ma9 L   2 IELTQPPSVSVVPGQTARISCSGDNIPYEYASWYQQKPGQAPVLVIYGDNNRPSGIPERFSGSNSGNTATLTISGTQAEDEADYYCASWDSMTVDGVFGGGTKLTVLGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAP 210
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201
   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  (1, 2)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3MA9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3MA9)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3MA9)

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  Cis Peptide Bonds
    Glu H:155 - Pro H:156   [ RasMol ]  
    Ile L:27 - Pro L:28   [ RasMol ]  
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    Tyr L:142 - Pro L:143   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/TrEMBL
        D0VWW0_9HIV1 | D0VWW0: 2cmr 2mk3 3mac

(-) Related Entries Specified in the PDB File

3mac CRYSTAL STRUCTURE OF GP41-DERIVED PROTEIN COMPLEXED WITH FAB 8062