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(-) Description

Title :  ENVELOPE GLYCOPROTEIN GP120 CORE FROM HIV TYPE 2 BOUND TO THE FIRST TWO DOMAINS OF HUMAN SOLUBLE CD4 RECEPTOR
 
Authors :  Y. W. Davenport, P. J. Bjorkman
Date :  30 Jun 15  (Deposition) - 09 Dec 15  (Release) - 10 Feb 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym./Biol. Unit :  B,G
Keywords :  Hiv-2, Gp120, Glycoprotein, Cd4, Viral Protein-Immune System Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Y. W. Davenport, A. P. West, P. J. Bjorkman
Structure Of An Hiv-2 Gp120 In Complex With Cd4.
J. Virol. V. 90 2112 2015
PubMed-ID: 26608312  |  Reference-DOI: 10.1128/JVI.02678-15

(-) Compounds

Molecule 1 - ENVELOPE GLYCOPROTEIN GP120 CORE FROM ST STRAIN OF HIV-2
    ChainsG
    EngineeredYES
    Expression SystemHOMO SAPIENS
    Expression System CommonHUMAN
    Expression System Taxid9606
    MutationYES
    Organism ScientificHUMAN IMMUNODEFICIENCY VIRUS TYPE 2 (ISOLATE ST)
    Organism Taxid11721
 
Molecule 2 - T-CELL SURFACE GLYCOPROTEIN CD4
    ChainsB
    EngineeredYES
    Expression SystemSPODOPTERA FRUGIPERDA
    Expression System CommonFALL ARMYWORM
    Expression System Taxid7108
    Expression System Vector TypeBACULOVIRUS
    FragmentDOMAINS 1 AND 2 (UNP RESIDUES 26-208)
    GeneCD4
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymT-CELL SURFACE ANTIGEN T4/LEU-3

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit BG

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 11)

Asymmetric/Biological Unit (2, 11)
No.NameCountTypeFull Name
1BMA1Ligand/IonBETA-D-MANNOSE
2NAG10Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER B:60 , ASP B:63 , ASN G:212binding site for residue NAG B 201
2AC2SOFTWAREASN G:79 , LYS G:498binding site for Mono-Saccharide NAG G 601 bound to ASN G 79
3AC3SOFTWAREALA G:68 , ASN G:244 , LYS G:257 , VAL G:259binding site for Mono-Saccharide NAG G 604 bound to ASN G 244
4AC4SOFTWAREGLY B:123 , GLN G:270 , ASN G:278 , ARG G:397 , ASN G:460 , SER G:461binding site for Poly-Saccharide residues NAG G 605 through BMA G 607 bound to ASN G 278
5AC5SOFTWAREASN G:284 , ASN G:302 , PHE G:304 , GLU G:356binding site for Mono-Saccharide NAG G 610 bound to ASN G 284
6AC6SOFTWAREGLU B:87 , LYS B:90 , ASP G:294 , ASN G:295 , LYS G:368 , GLY G:472binding site for Poly-Saccharide residues NAG G 602 through NAG G 603 bound to ASN G 295
7AC7SOFTWAREASN G:306binding site for Mono-Saccharide NAG G 609 bound to ASN G 306
8AC8SOFTWAREGLU G:383 , TYR G:391 , ASN G:404 , THR G:406binding site for Mono-Saccharide NAG G 608 bound to ASN G 404

(-) SS Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1B:16 -B:84
2B:130 -B:159
3G:101 -G:220
4G:233 -G:263
5G:243 -G:255
6G:311 -G:344
7G:396 -G:459
8G:403 -G:432

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Asp G:60 -Asn G:61
2Pro G:314 -Gly G:315
3Tyr G:367 -Lys G:368

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5CAY)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5CAY)

(-) Exons   (0, 0)

(no "Exon" information available for 5CAY)

(-) 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 B from PDB  Type:PROTEIN  Length:150
                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeee.....eee............eee.....eeeeee..eee.........ee.hhhhhhhh...eee...hhhhheeeeee....eeeeeeee.eee....eee.......eeeee......ee......eeeee....ee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5cay B   2 KVVLGKKGDTVELTCTASQKKSIQFHWKNSNQIKILGNQGSFLTKGPSKLNDRADSRRSLWDQGNFPLIIKNLKIEDSDTYICEVEDQKEEVQLLVFGLTALTLTLESPPGSSPSVQCRSPRGKNIQGGKTLWTCTVLQNQKKVEFKIDI 174
                                    11        21        31        41        51        61        71        81        91       101||     122       132       142 ||    164       174
                                                                                                                              102|                           144|                 
                                                                                                                               114                            157                 

Chain G from PDB  Type:PROTEIN  Length:311
                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee........eeee...eeee...hhhhhhhhhhhhhhhhhhh...eee....eee...........eeeee....eeeeee.......eeeee..eeee.....ee......eee.........eeee.....eeeee.......eeeeee......eeeee...hhhhhhhhhhhhhhh............eeee......hhhhhheeeee..eeeee.hhhhhhh......eeeeeee.eee......eee........eeeeeeeeeeeeeee....eeeee...hhhhhhhhhh.eeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5cay G  41 PLFCATKDNDDYQEIALNVIEAFDAWNNTVTEQAVEDVWSLFETSIKPCVKLTNTSVITESCDKHYWDTMRFRYCAPPGFALLRCNDTNYSGFEPNCSKVVAATCTRMMETQTSTWFGFNGTRAENRTYIYWHGRDNRTIISLNKFYNLTVHCKRPGRRPRQAWCWFKGEWKEAMKEVKLTLAKHPRYKGTNDTEKIRFIAPGERSDPEVAYMWTNCRGEFLYCNMTWFLNWVENQHNYVPCHIKQIINTWHKVGKNVYLPPREGQLTCNSTVTSIIANIDGGEQTNITFSAEVAELYRLELGDYKLIEVT 503
                                  ||62        72        82        92       102  ||   218       228       238       248       258       268       278       288       298       308      |339       349       359       369       379       389       399       409    || 430       440       450       460       470   ||  482       492       502 
                                 47|                                          105|                                                                                                    315|                                                                          414|                                             474|                          
                                  60                                           212                                                                                                     337                                                                           426                                              477                          

   Legend:   → Mismatch (orange background)
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  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 5CAY)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5CAY)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5CAY)

(-) Gene Ontology  (73, 76)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Asp G:60 - Asn G:61   [ RasMol ]  
    Pro G:314 - Gly G:315   [ RasMol ]  
    Tyr G:367 - Lys G:368   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        CD4_HUMAN | P017301cdh 1cdi 1cdj 1cdu 1cdy 1g9m 1g9n 1gc1 1jl4 1opn 1opt 1opw 1q68 1rzj 1rzk 1wbr 1wio 1wip 1wiq 2b4c 2jkr 2jkt 2klu 2nxy 2nxz 2ny0 2ny1 2ny2 2ny3 2ny4 2ny5 2ny6 2qad 3b71 3cd4 3j70 3jcb 3jcc 3jwd 3jwo 3lqa 3o2d 3s4s 3s5l 3t0e 4h8w 4jm2 4p9h 4q6i 4r2g 4r4h 4rqs 5a7x 5a8h 5thr 5u1f 5vn3

(-) Related Entries Specified in the PDB File

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