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(-) Description

Title :  CRYSTAL STRUCTURE OF CD4M47, A SCORPION-TOXIN MIMIC OF CD4, IN COMPLEX WITH HIV-1 YU2 GP120 ENVELOPE GLYCOPROTEIN AND ANTI-HIV-1 ANTIBODY 17B
 
Authors :  C. -C. Huang, P. D. Kwong
Date :  26 Aug 06  (Deposition) - 10 Oct 06  (Release) - 06 Jun 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  G,H,L,M,P,Q,R,S
Biol. Unit 1:  G,H,L,M  (1x)
Biol. Unit 2:  P,Q,R,S  (1x)
Keywords :  Hiv-1, Gp120, Yu2, Scorpion Toxin, Cd4 Mimic, Cd4M47, Antibody, Viral Protein-Immune System Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  F. Stricher, C. C. Huang, A. Descours, S. Duquesnoy, O. Combes, J. M. Decker, Y. D. Kwon, P. Lusso, G. M. Shaw, C. Vita, P. D. Kwong, L. Martin
Combinatorial Optimization Of A Cd4-Mimetic Miniprotein And Cocrystal Structures With Hiv-1 Gp120 Envelope Glycoprotein
J. Mol. Biol. V. 382 510 2008
PubMed-ID: 18619974  |  Reference-DOI: 10.1016/J.JMB.2008.06.069

(-) Compounds

Molecule 1 - EXTERIOR MEMBRANE GLYCOPROTEIN(GP120)
    ChainsG, P
    EngineeredYES
    Expression SystemDROSOPHILA MELANOGASTER
    Expression System CommonFRUIT FLY
    Expression System Taxid7227
    FragmentCORE
    GeneENV
    Organism ScientificHUMAN IMMUNODEFICIENCY VIRUS
    Organism Taxid12721
    StrainYU2
    SynonymHIV-1 YU2 GP120
 
Molecule 2 - ANTIBODY 17B LIGHT CHAIN
    ChainsL, Q
    EngineeredYES
    Expression SystemHUMAN HERPESVIRUS 4
    Expression System CommonEPSTEIN-BARR VIRUS
    Expression System Taxid10376
    FragmentANTIGEN-BINDING FRAGMENT, FAB
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
 
Molecule 3 - ANTIBODY 17B HEAVY CHAIN
    ChainsH, R
    EngineeredYES
    Expression SystemHUMAN HERPESVIRUS 4
    Expression System CommonEPSTEIN-BARR VIRUS
    Expression System Taxid10376
    FragmentANTIGEN-BINDING FRAGMENT, FAB
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
 
Molecule 4 - CD4M47, SCORPION-TOXIN MIMIC OF CD4
    ChainsM, S
    EngineeredYES
    Organism ScientificSYNTHETIC
    Organism Taxid32630
    Other DetailsTHIS PROTEIN IS A MIMIC OF THE PROTEIN THAT OCCURS NATURALLY IN LEIURUS QUINQUESTRIATUS HEBRAEUS (ISRAELI SCORPION).
    SyntheticYES

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit GHLMPQRS
Biological Unit 1 (1x)GHLM    
Biological Unit 2 (1x)    PQRS

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 24)

Asymmetric Unit (6, 24)
No.NameCountTypeFull Name
1BIF2Mod. Amino Acid(R)-2-AMINO-3-(4-PHENYLCYCLOHEXYL)PROPANOIC ACID
2DPR2Mod. Amino AcidD-PROLINE
3MPT2Mod. Amino AcidBETA-MERCAPTOPROPIONIC ACID
4NAG14Ligand/IonN-ACETYL-D-GLUCOSAMINE
5NDG2Ligand/Ion2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
6VLM2Mod. Amino AcidVALINYLAMINE
Biological Unit 1 (5, 12)
No.NameCountTypeFull Name
1BIF1Mod. Amino Acid(R)-2-AMINO-3-(4-PHENYLCYCLOHEXYL)PROPANOIC ACID
2DPR1Mod. Amino AcidD-PROLINE
3MPT1Mod. Amino AcidBETA-MERCAPTOPROPIONIC ACID
4NAG8Ligand/IonN-ACETYL-D-GLUCOSAMINE
5NDG-1Ligand/Ion2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
6VLM1Mod. Amino AcidVALINYLAMINE
Biological Unit 2 (6, 12)
No.NameCountTypeFull Name
1BIF1Mod. Amino Acid(R)-2-AMINO-3-(4-PHENYLCYCLOHEXYL)PROPANOIC ACID
2DPR1Mod. Amino AcidD-PROLINE
3MPT1Mod. Amino AcidBETA-MERCAPTOPROPIONIC ACID
4NAG6Ligand/IonN-ACETYL-D-GLUCOSAMINE
5NDG2Ligand/Ion2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
6VLM1Mod. Amino AcidVALINYLAMINE

(-) Sites  (16, 16)

Asymmetric Unit (16, 16)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN G:88 , ASN G:241BINDING SITE FOR RESIDUE NAG G 588
02AC2SOFTWAREASN G:234 , THR G:236 , SER G:274 , HOH G:950BINDING SITE FOR RESIDUE NAG G 734
03AC3SOFTWAREASP G:230 , LYS G:231 , ASN G:241BINDING SITE FOR RESIDUE NAG G 741
04AC4SOFTWAREARG G:252 , ASN G:262 , ASN G:377 , CYS G:378 , CYS G:445 , SER G:446 , SER G:447 , HOH G:942BINDING SITE FOR RESIDUE NAG G 762
05AC5SOFTWAREASN G:276 , THR G:278 , ASN G:279 , LYS P:460BINDING SITE FOR RESIDUE NAG G 776
06AC6SOFTWAREGLU G:268 , GLU G:269 , ILE G:270 , ASN G:289 , GLU G:290 , GLN G:344 , LYS L:188BINDING SITE FOR RESIDUE NAG G 789
07AC7SOFTWAREGLU G:87 , ASN G:295 , SER G:446BINDING SITE FOR RESIDUE NAG G 795
08AC8SOFTWAREASN G:386 , THR G:388 , GLY S:14BINDING SITE FOR RESIDUE NAG G 886
09AC9SOFTWAREASN P:88 , THR P:240 , ASN P:241 , NDG P:741 , HOH P:932BINDING SITE FOR RESIDUE NAG P 588
10BC1SOFTWAREASN P:234 , THR P:236BINDING SITE FOR RESIDUE NAG P 734
11BC2SOFTWAREASP P:230 , LYS P:231 , ASN P:241 , NAG P:588BINDING SITE FOR RESIDUE NDG P 741
12BC3SOFTWAREASN P:262 , ASN P:377 , CYS P:378 , SER P:446 , SER P:447 , HOH P:905 , HOH P:920BINDING SITE FOR RESIDUE NAG P 762
13BC4SOFTWARELYS G:460 , ASN P:276 , THR P:278 , ASN P:279BINDING SITE FOR RESIDUE NAG P 776
14BC5SOFTWAREGLU P:267 , GLU P:268 , GLU P:269 , ILE P:270 , ASN P:289 , GLN P:344BINDING SITE FOR RESIDUE NDG P 789
15BC6SOFTWAREGLU P:87 , ASN P:295 , SER P:446BINDING SITE FOR RESIDUE NAG P 795
16BC7SOFTWAREASP G:461 , THR G:462 , ASN P:386 , THR P:388 , GLN P:389BINDING SITE FOR RESIDUE NAG P 886

(-) SS Bonds  (26, 26)

Asymmetric Unit
No.Residues
1G:119 -G:205
2G:126 -G:196
3G:218 -G:247
4G:228 -G:239
5G:296 -G:331
6G:378 -G:445
7G:385 -G:418
8H:22 -H:92
9H:140 -H:196
10L:23 -L:88
11L:134 -L:194
12M:6 -M:24
13M:10 -M:26
14P:119 -P:205
15P:126 -P:196
16P:218 -P:247
17P:228 -P:239
18P:296 -P:331
19P:378 -P:445
20P:385 -P:418
21Q:23 -Q:88
22Q:134 -Q:194
23R:22 -R:92
24R:140 -R:196
25S:6 -S:24
26S:10 -S:26

(-) Cis Peptide Bonds  (10, 10)

Asymmetric Unit
No.Residues
1Ser L:7 -Pro L:8
2Trp L:94 -Pro L:95
3Tyr L:140 -Pro L:141
4Phe H:146 -Pro H:147
5Glu H:148 -Pro H:149
6Ser Q:7 -Pro Q:8
7Trp Q:94 -Pro Q:95
8Tyr Q:140 -Pro Q:141
9Phe R:146 -Pro R:147
10Glu R:148 -Pro R:149

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2I5Y)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2I5Y)

(-) Exons   (0, 0)

(no "Exon" information available for 2I5Y)

(-) Sequences/Alignments

Asymmetric 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 G from PDB  Type:PROTEIN  Length:302
 aligned with ENV_HV1Y2 | P35961 from UniProtKB/Swiss-Prot  Length:843

    Alignment length:399
                                    90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470         
           ENV_HV1Y2     81 QEVKLENVTENFNMWKNNMVEQMHEDIISLWDQSLKPCVKLTPLCVTLNCTDLRNATNTTSSSWETMEKGEIKNCSFNITTSIRDKVQKEYALFYNLDVVPIDNASYRLISCNTSVITQACPKVSFEPIPIHYCAPAGFAILKCNDKKFNGTGPCTNVSTVQCTHGIRPVVSTQLLLNGSLAEEEIVIRSENFTNNAKTIIVQLNESVVINCTRPNNNTRKSINIGPGRALYTTGEIIGDIRQAHCNLSKTQWENTLEQIAIKLKEQFGNNKTIIFNPSSGGDPEIVTHSFNCGGEFFYCNSTQLFTWNDTRKLNNTGRNITLPCRIKQIINMWQEVGKAMYAPPIRGQIRCSSNITGLLLTRDGGKDTNGTEIFRPGGGDMRDNWRSELYKYKVVKIE  479
               SCOP domains d2i5yg_ G: gp120 core                                                                                                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains 2i5yG00 G:82-492 HIV Envelope Protein Gp120; Cha                                                             in G                                                                                                                                                                                                                                                                                               CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eee...hhhhhhhhhhhhhhhhh.....eeeeeee...-------------------------------------------------------------..eeeeeee....................eeeeee.......eee...eeee.............eee.........eeee.........eeeeeeeeeeeee...----------------------------.eeeeehhhhhhhhhhhhhhhhhhhh...eeee......hhhhhheeeee..eeeee.......ee.--------.eeeeeeee..eee......eee..........eeeeeeeeeeee........eeeeee...hhhhhhhhhhh.eeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2i5y G   82 SEVKLENVTENFNMWKNNMVEQMHEDIISLWDQSLKPCVKLTPLCVGA-------------------------------------------------------------GSCNTSVITQACPKVSFEPIPIHYCAPAGFAILKCNDKKFNGTGPCTNVSTVQCTHGIRPVVSTQLLLNGSLAEEEIVIRSENFTNNAKTIIVQLNESVVINCTGA----------------------------GHCNLSKTQWENTLEQIAIKLKEQFGNNKTIIFNPSSGGDPEIVTHSFNCGGEFFYCNSTQLFTWND--------RNITLPCRIKQIINMWQEVGKAMYAPPIRGQIRCSSNITGLLLTRDGGKDTNGTEIFRPGGGDMRDNWRSELYKYKVVKIE  492
                                    91       101       111       121       | -         -         -         -         -         -       194       204       214       224       234       244       254       264       274       284       294    |    -         -         -   |   335       345       355       365       375       385       395       413       423       433       443       453       463       473       483         
                                                                         129                                                           194                                                                                                      299                          329                                                               395      412                                                                                

Chain H from PDB  Type:PROTEIN  Length:224
 aligned with Q5EBM2_HUMAN | Q5EBM2 from UniProtKB/TrEMBL  Length:519

    Alignment length:230
                                                                                                                                        130    131                                                                                                                
                                    29        39        49        59        69        79        89        99       109       119       129|      133       143       153       163       173       183       193       203       213       223       233       243
        Q5EBM2_HUMAN     20 QVQLVQSGAEVKKPGASVKVSCEVSGHTLTELSRHWVRQAPGKGLEWMGGFDPEDGETVYAQTFQGRVTMTEDTSTDTAYMDLSNLRSDDTAVYYCATGVYDVLTGYSRFD------YWGQGTQVTVSSASTKGPSVFPLAPCSRSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYTCNVNHKPSNTKVDKRVELK  243
               SCOP domains d2i5yh1 H:1-113 Immunoglobulin heavy chain variable domain, VH                                                                   d2i5yh2 H:114-     214 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                  SCOP domains
               CATH domains 2i5yH01 H:1-113 Immunoglobulins                                                                                                  2i5yH02 H:114-     213 Immunoglobulins                                                              - CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee..hhh.eeeeeeee......eeeeeee....eeee.......eeeeee....eeeeee...hhhhheeeeee-eee..hhhhh.........ee...eeeee........eeeee...-----..eeeeeeeeeee.....eeee.........ee...ee.....eeeeeeeeee.hhh.....eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2i5y H    1 EVQLVESGAEVKKPGSSVKVSCKASGDTFIRYSFTWVRQAPGQGLEWMGRIITILDVAHYAPHLQGRVTITADKSTSTVYLELRNLRSDDTAVYFCA-GVYEGEADEGEYDNNGFLKHWGQGTLVTVSSASTKGPSVFPLAPS-----GGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPK  214
                                    10        20        30        40        50  |     59        69        79   |||  86      | 95     |100E|||||| 104       114       124  |    134       144       154       164       174       184       194       204       214
                                                                              52A                            82A||         93 |   100A|||||100J|                        127   133                                                                                 
                                                                                                              82B|           94    100B|||||100K                                                                                                                  
                                                                                                               82C                  100C||||||                                                                                                                    
                                                                                                                                     100D|||||                                                                                                                    
                                                                                                                                      100E||||                                                                                                                    
                                                                                                                                       100F|||                                                                                                                    
                                                                                                                                        100G||                                                                                                                    
                                                                                                                                         100H|                                                                                                                    
                                                                                                                                          100I                                                                                                                    

Chain L from PDB  Type:PROTEIN  Length:214
                                                                                                                                                                                                                                                       
               SCOP domains d2i5yl1 L:1-107 Immunoglobulin light chain kappa variable domain, VL-kappa                                   d2i5yl2 L:108-212 Immunoglobulin light chain kappa constant domain, CL-kappa                              SCOP domains
               CATH domains 2i5yL01 L:1-108 Immunoglobulins                                                                               2i5yL02 L:109-211 Immunoglobulins                                                                      - CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhh.eeeeee........ee...eeeee.......eeeee..hhhhhhhheeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhh...eeeeeee.......eeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2i5y L    1 DIVMTQSPATLSVSPGERATLSCRASESVSSDLAWYQQKPGQAPRLLIYGASTRATGVPARFSGSGSGAEFTLTISSLQSEDFAVYYCQQYNNWPPRYTFGQGTRLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRG  212
                                    10        20        30        40        50        60        70        80        90     || 98       108       118       128       138       148       158       168       178       188       198       208    
                                                                                                                         95A|                                                                                                                     
                                                                                                                          95B                                                                                                                     

Chain M from PDB  Type:PROTEIN  Length:27
                                                            
               SCOP domains -d2i5ym1 M:2-27             SCOP domains
               CATH domains --------------------------- CATH domains
               Pfam domains --------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhh...eeeee..eeeee Sec.struct. author
                 SAPs(SNPs) --------------------------- SAPs(SNPs)
                    PROSITE --------------------------- PROSITE
                 Transcript --------------------------- Transcript
                2i5y M    1 xNLHFCQLRCKSLGLLGRCAxTfCACx   27
                            |       10        20| |   |
                            1-MPT              21-DPR |
                                                 23-BIF
                                                     27-VLM

Chain P from PDB  Type:PROTEIN  Length:300
 aligned with ENV_HV1Y2 | P35961 from UniProtKB/Swiss-Prot  Length:843

    Alignment length:399
                                    90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470         
           ENV_HV1Y2     81 QEVKLENVTENFNMWKNNMVEQMHEDIISLWDQSLKPCVKLTPLCVTLNCTDLRNATNTTSSSWETMEKGEIKNCSFNITTSIRDKVQKEYALFYNLDVVPIDNASYRLISCNTSVITQACPKVSFEPIPIHYCAPAGFAILKCNDKKFNGTGPCTNVSTVQCTHGIRPVVSTQLLLNGSLAEEEIVIRSENFTNNAKTIIVQLNESVVINCTRPNNNTRKSINIGPGRALYTTGEIIGDIRQAHCNLSKTQWENTLEQIAIKLKEQFGNNKTIIFNPSSGGDPEIVTHSFNCGGEFFYCNSTQLFTWNDTRKLNNTGRNITLPCRIKQIINMWQEVGKAMYAPPIRGQIRCSSNITGLLLTRDGGKDTNGTEIFRPGGGDMRDNWRSELYKYKVVKIE  479
               SCOP domains d2i5yp_ P: gp120 core                                                                                                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains 2i5yP00 P:82-492 HIV Envelope Protein Gp120; Cha                                                             in G                                                                                                                                                                                                                                                                                               CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeee...hhhhhhhhhhhhhhhhhhh...eeee......-------------------------------------------------------------.....eeee....................eeeeee.......eeee..eeee.............eee.........eee..........eeeeeeeeeeeee...----------------------------.eeeeehhhhhhhhhhhhhhhhhhhh...eeee......hhhhhheeeee..eeeee.hhhhh..----------.eeeeeeeee.eee......eee..........eeeeeeeeeeeee.......eeeeee...hhhhhhhhhhh.eeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2i5y P   82 SEVKLENVTENFNMWKNNMVEQMHEDIISLWDQSLKPCVKLTPLCVGA-------------------------------------------------------------GSCNTSVITQACPKVSFEPIPIHYCAPAGFAILKCNDKKFNGTGPCTNVSTVQCTHGIRPVVSTQLLLNGSLAEEEIVIRSENFTNNAKTIIVQLNESVVINCTGA----------------------------GHCNLSKTQWENTLEQIAIKLKEQFGNNKTIIFNPSSGGDPEIVTHSFNCGGEFFYCNSTQLFTW----------RNITLPCRIKQIINMWQEVGKAMYAPPIRGQIRCSSNITGLLLTRDGGKDTNGTEIFRPGGGDMRDNWRSELYKYKVVKIE  492
                                    91       101       111       121       | -         -         -         -         -         -       194       204       214       224       234       244       254       264       274       284       294    |    -         -         -   |   335       345       355       365       375       385       | -       413       423       433       443       453       463       473       483         
                                                                         129                                                           194                                                                                                      299                          329                                                             393        412                                                                                

Chain Q from PDB  Type:PROTEIN  Length:214
                                                                                                                                                                                                                                                       
               SCOP domains d2i5yq1 Q:1-107 Immunoglobulin light chain kappa variable domain, VL-kappa                                   d2i5yq2 Q:108-212 Immunoglobulin light chain kappa constant domain, CL-kappa                              SCOP domains
               CATH domains 2i5yQ01 Q:1-108 Immunoglobulins                                                                               2i5yQ02 Q:109-211 Immunoglobulins                                                                      - CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhh.eeeeee........ee...eeeee.......eeeee..hhhhhhhheeeeeeeeeee.....eeeeee........eeeee.........eeeeeeeeeehhhhhh..eeeeeee.......eeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2i5y Q    1 DIVMTQSPATLSVSPGERATLSCRASESVSSDLAWYQQKPGQAPRLLIYGASTRATGVPARFSGSGSGAEFTLTISSLQSEDFAVYYCQQYNNWPPRYTFGQGTRLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRG  212
                                    10        20        30        40        50        60        70        80        90     || 98       108       118       128       138       148       158       168       178       188       198       208    
                                                                                                                         95A|                                                                                                                     
                                                                                                                          95B                                                                                                                     

Chain R from PDB  Type:PROTEIN  Length:223
 aligned with Q5EBM2_HUMAN | Q5EBM2 from UniProtKB/TrEMBL  Length:519

    Alignment length:230
                                                                                                                                        130    131                                                                                                                
                                    29        39        49        59        69        79        89        99       109       119       129|      133       143       153       163       173       183       193       203       213       223       233       243
        Q5EBM2_HUMAN     20 QVQLVQSGAEVKKPGASVKVSCEVSGHTLTELSRHWVRQAPGKGLEWMGGFDPEDGETVYAQTFQGRVTMTEDTSTDTAYMDLSNLRSDDTAVYYCATGVYDVLTGYSRFD------YWGQGTQVTVSSASTKGPSVFPLAPCSRSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYTCNVNHKPSNTKVDKRVELK  243
               SCOP domains d2i5yr1 R:1-113 Immunoglobulin heavy chain variable domain, VH                                                                   d2i5yr2 R:114-      214 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                 SCOP domains
               CATH domains 2i5yR01 R:1-113 Immunoglobulins                                                                                                  2i5yR02 R:114-      213 Immunoglobulins                                                             - CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee..hhh.eeeeeeee......eeeeee.hhhh.eee.......eeeeee....eeeeee...hhhhheeeeee-eee..hhhhh.........ee...eeeee........eeeee...------.eeeeeeeeeee.....eeee.hhh.....ee...ee.....eeeeeeeeee.hhh.....eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2i5y R    1 EVQLVESGAEVKKPGSSVKVSCKASGDTFIRYSFTWVRQAPGQGLEWMGRIITILDVAHYAPHLQGRVTITADKSTSTVYLELRNLRSDDTAVYFCA-GVYEGEADEGEYDNNGFLKHWGQGTLVTVSSASTKGPSVFPLAPS------GTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPK  214
                                    10        20        30        40        50  |     59        69        79   |||  86      | 95     |100E|||||| 104       114       124  |    134       144       154       164       174       184       194       204       214
                                                                              52A                            82A||         93 |   100A|||||100J|                        127    134                                                                                
                                                                                                              82B|           94    100B|||||100K                                                                                                                  
                                                                                                               82C                  100C||||||                                                                                                                    
                                                                                                                                     100D|||||                                                                                                                    
                                                                                                                                      100E||||                                                                                                                    
                                                                                                                                       100F|||                                                                                                                    
                                                                                                                                        100G||                                                                                                                    
                                                                                                                                         100H|                                                                                                                    
                                                                                                                                          100I                                                                                                                    

Chain S from PDB  Type:PROTEIN  Length:27
                                                            
               SCOP domains -d2i5ys1 S:2-27             SCOP domains
               CATH domains --------------------------- CATH domains
               Pfam domains --------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh..eeeee..eeeee Sec.struct. author
                 SAPs(SNPs) --------------------------- SAPs(SNPs)
                    PROSITE --------------------------- PROSITE
                 Transcript --------------------------- Transcript
                2i5y S    1 xNLHFCQLRCKSLGLLGRCAxTfCACx   27
                            |       10        20| |   |
                            1-MPT              21-DPR |
                                                 23-BIF
                                                     27-VLM

   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  (6, 12)

Asymmetric Unit

(-) CATH Domains  (2, 10)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2I5Y)

(-) Gene Ontology  (41, 41)

Asymmetric Unit(hide GO term definitions)
Chain G,P   (ENV_HV1Y2 | P35961)
molecular function
    GO:0005198    structural molecule activity    The action of a molecule that contributes to the structural integrity of a complex or its assembly within or outside a cell.
biological process
    GO:0075512    clathrin-dependent endocytosis of virus by host cell    Any clathrin-mediated endocytosis that is involved in the uptake of a virus into a host cell. Begins by invagination of a specific region of the host cell plasma membrane around the bound virus to form a clathrin-coated pit, which then pinches off to form a clathrin-coated endocytic vesicle containing the virus.
    GO:0075509    endocytosis involved in viral entry into host cell    Any endocytosis that is involved in the uptake of a virus into a host cell.
    GO:0030683    evasion or tolerance by virus of host immune response    Any process, either active or passive, by which a virus avoids the effects of the host organism's immune response. The host is defined as the larger of the organisms involved in a symbiotic interaction.
    GO:0039654    fusion of virus membrane with host endosome membrane    Fusion of a virus membrane with a host endosome membrane. Occurs after internalization of the virus through the endosomal pathway, and results in release of the virus contents into the cell.
    GO:0019064    fusion of virus membrane with host plasma membrane    Fusion of a viral membrane with the host cell membrane during viral entry. Results in release of the virion contents into the cytoplasm.
    GO:0039663    membrane fusion involved in viral entry into host cell    Merging of the virion membrane and a host membrane (host plasma membrane or host organelle membrane) that is involved in the uptake of a virus into a host cell.
    GO:0002223    stimulatory C-type lectin receptor signaling pathway    Any series of molecular signals generated as a consequence of binding to a C-type lectin receptor capable of cellular activation.
    GO:0046718    viral entry into host cell    The process that occurs after viral attachment by which a virus, or viral nucleic acid, breaches the plasma membrane or cell envelope and enters the host cell. The process ends when the viral nucleic acid is released into the host cell cytoplasm.
    GO:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
    GO:0019082    viral protein processing    Any protein maturation process achieved by the cleavage of a peptide bond or bonds within a viral protein.
    GO:0019062    virion attachment to host cell    The process by which a virion protein binds to molecules on the host cellular surface or host cell surface projection.
cellular component
    GO:0044174    host cell endosome    A membrane-bounded organelle that carries materials newly ingested by endocytosis. It passes many of the materials to host cell lysosomes for degradation.
    GO:0044175    host cell endosome membrane    The lipid bilayer surrounding a host cell endosome.
    GO:0033644    host cell membrane    Double layer of lipid molecules as it encloses host cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins. The host is defined as the larger of the organisms involved in a symbiotic interaction.
    GO:0020002    host cell plasma membrane    The plasma membrane surrounding a host cell.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0019031    viral envelope    The lipid bilayer of a virion that surrounds the protein capsid. May also contain glycoproteins.
    GO:0019012    virion    The complete fully infectious extracellular virus particle.
    GO:0055036    virion membrane    The lipid bilayer surrounding a virion.

Chain H,R   (Q5EBM2_HUMAN | Q5EBM2)

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 Related Entries

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

UniProtKB/Swiss-Prot
        ENV_HV1Y2 | P359611g9n 1rzk 1yyl 1yym 2i60 2ny7 2qad 3hi1 3tgq 4dvr 4jo3 4jzw 4jzz 4k0a 4ka2 4laj 4r4f 4rqs 4rwy 5a7x 5a8h
        IGHG1_HUMAN | P018571aj7 1aqk 1axs 1bey 1d5b 1d5i 1d6v 1dfb 1dn2 1e4k 1fc1 1fc2 1fcc 1gaf 1h3t 1h3u 1h3v 1h3w 1h3x 1h3y 1hkl 1hzh 1i7z 1l6x 1n7m 1op3 1oqo 1oqx 1pg7 1t83 1t89 1vge 2dts 2gj7 2iwg 2j6e 2jb5 2jb6 2o5x 2o5y 2o5z 2osl 2qad 2ql1 2qqk 2qql 2qqn 2qr0 2r56 2rcj 2rcs 2vxq 2wah 3agv 3ave 3ay4 3b2u 3b2v 3bdy 3be1 3bky 3bn9 3bqu 3c08 3c09 3c2s 3cfj 3cfk 3csy 3d0l 3d0v 3d6g 3d85 3dj9 3dnk 3do3 3dro 3drq 3dvg 3dvn 3eyf 3eyo 3eyq 3fjt 3mcl 3o11 3ry6 3s7g 3sgj 3sgk 3tv3 3twc 3tyg 3u0w 3u7w 3u7y 3v7m 3v8c 3v95 3wjj 3wjl 3wkn 3wn5 4acp 4b7i 4bm7 4bsv 4bsw 4byh 4cdh 4d9q 4d9r 4dag 4dz8 4eow 4hix 4j12 4ku1 4lld 4llm 4llq 4n0u 4nqs 4nqt 4nqu 4nwt 4nwu 4o4y 4o51 4q6y 4q74 4q7d 4w4n 4w4o 4wi2 4wi3 4wi4 4wi5 4wi6 4wi7 4wi8 4wi9 4x4m 4x98 4x99 4xmp 4xny 4xnz 4xxd 4zne 5bw7 5c7k 5d4q 5d6d 5di8 5dj0 5dj2 5dj6 5dj8 5dja 5djc 5djd 5djx 5djy 5djz 5dk0 5dk2 5dvk 5dvl 5dvm 5dvn 5dvo 5gsq 5hsf 5hy9 5hye 5hyf 5hyi 5iq7 5iq9 5iw3 5iw6 5jih 5jii 5jik 5k33 5k8d 5kwg 5m3v 5v43 5v4e

(-) Related Entries Specified in the PDB File

1yyl CRYSTAL STRUCTURE OF CD4M33, A SCORPION-TOXIN MIMIC OF CD4, IN COMPLEX WITH HIV-1 YU2 GP120 ENVELOPE GLYCOPROTEIN AND ANTI-HIV-1 ANTIBODY 17B
1yym CRYSTAL STRUCTURE OF F23, A SCORPION-TOXIN MIMIC OF CD4, IN COMPLEX WITH HIV-1 YU2 GP120 ENVELOPE GLYCOPROTEIN AND ANTI -HIV-1 ANTIBODY 17B
2i60 CRYSTAL STRUCTURE OF [PHE23]M47, A SCORPION-TOXIC MIMIC OF CD4, IN COMPLEX WITH HIV-1 YU2 GP120 ENVELOPE GLYCOPROTEIN AND ANTI-HIV-1 ANTIBODY 17B