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(-) Description

Title :  CRYSTAL STRUCTURE OF CLADE A/E 93TH057 HIV-1 GP120 CORE IN COMPLEX WITH TS-II-224
 
Authors :  Y. D. Kwon, J. M. Lalonde, D. M. Jones, A. W. Sun, J. R. Courter, T. Soeta, T. Kobayashi, A. M. Princiotto, X. Wu, J. Mascola, A. Schon, E. Freire, J. Sodroski, N. Madani, A. B. Smith Iii, P. D. Kwong
Date :  03 Feb 12  (Deposition) - 02 May 12  (Release) - 20 Jun 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.98
Chains :  Asym. Unit :  A,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  C  (1x)
Keywords :  Hiv-1 Gp120, Clade A/E, Cd4 Mimic, Ts-Ii-224, Viral Protein-Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. M. Lalonde, Y. D. Kwon, D. M. Jones, A. W. Sun, J. R. Courter, T. Soeta, T. Kobayashi, A. M. Princiotto, X. Wu, A. Schon, E. Freire, P. D. Kwong, J. R. Mascola, J. Sodroski, N. Madani, A. B. Smith
Structure-Based Design, Synthesis, And Characterization Of Dual Hotspot Small-Molecule Hiv-1 Entry Inhibitors.
J. Med. Chem. V. 55 4382 2012
PubMed-ID: 22497421  |  Reference-DOI: 10.1021/JM300265J

(-) Compounds

Molecule 1 - HIV-1 GP120 CORE
    Chains: A, C
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Plasmid: PVRC8400
    Expression System Strain: 293F
    Expression System Taxid: 9606
    Expression System Vector Type: PLASMID
    Gene: HIV-1 ENV
    Organism Common: HIV-1
    Organism Scientific: HUMAN IMMUNODEFICIENCY VIRUS TYPE 1
    Organism Taxid: 11686
    Strain: CLADE A/E 93TH057

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AC
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 26)

Asymmetric Unit (3, 26)
No.NameCountTypeFull Name
10LM2Ligand/IonN-(4-CHLORO-3-FLUOROPHENYL)-N'-(1,2,2,6,6-PENTAMETHYLPIPERIDIN-4-YL)ETHANEDIAMIDE
2EPE2Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
3NAG22Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 1 (3, 13)
No.NameCountTypeFull Name
10LM1Ligand/IonN-(4-CHLORO-3-FLUOROPHENYL)-N'-(1,2,2,6,6-PENTAMETHYLPIPERIDIN-4-YL)ETHANEDIAMIDE
2EPE1Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
3NAG11Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 2 (3, 13)
No.NameCountTypeFull Name
10LM1Ligand/IonN-(4-CHLORO-3-FLUOROPHENYL)-N'-(1,2,2,6,6-PENTAMETHYLPIPERIDIN-4-YL)ETHANEDIAMIDE
2EPE1Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
3NAG11Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (26, 26)

Asymmetric Unit (26, 26)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:234 , THR A:236 , ILE A:272 , HIS A:352BINDING SITE FOR RESIDUE NAG A 501
02AC2SOFTWAREASN A:241 , HOH A:766BINDING SITE FOR RESIDUE NAG A 502
03AC3SOFTWARELYS A:252 , ASN A:262 , ARG A:379 , CYS A:445 , VAL A:446 , SER A:447 , NAG A:511 , HOH A:617 , HOH A:633 , HOH A:644 , HOH A:716BINDING SITE FOR RESIDUE NAG A 503
04AC4SOFTWAREASN A:276 , ASN A:279 , HIS C:61BINDING SITE FOR RESIDUE NAG A 504
05AC5SOFTWAREGLU A:269 , ILE A:270 , ASN A:289 , LYS A:348 , HOH A:688BINDING SITE FOR RESIDUE NAG A 505
06AC6SOFTWAREASN A:295 , TYR A:330 , GLU A:332 , HOH A:660BINDING SITE FOR RESIDUE NAG A 506
07AC7SOFTWAREASN A:334 , THR A:336 , LYS A:337BINDING SITE FOR RESIDUE NAG A 507
08AC8SOFTWAREASN A:354 , ASN A:355 , PRO C:214 , LYS C:252BINDING SITE FOR RESIDUE NAG A 508
09AC9SOFTWAREASN A:386 , THR A:388BINDING SITE FOR RESIDUE NAG A 509
10BC1SOFTWAREGLN A:389 , ASN A:392 , THR A:394 , CYS A:395BINDING SITE FOR RESIDUE NAG A 510
11BC2SOFTWAREASN A:262 , SER A:291 , ASN A:448 , NAG A:503BINDING SITE FOR RESIDUE NAG A 511
12BC3SOFTWARELEU A:52 , CYS A:54 , ALA A:73 , GLN A:103 , ASP A:107BINDING SITE FOR RESIDUE EPE A 512
13BC4SOFTWAREVAL A:255 , SER A:256 , THR A:257 , GLU A:370 , SER A:375 , PHE A:382 , ASN A:425 , MET A:426 , TRP A:427 , GLY A:429 , GLY A:473 , ASN A:474BINDING SITE FOR RESIDUE 0LM A 513
14BC5SOFTWAREASN C:234 , THR C:236 , HIS C:352BINDING SITE FOR RESIDUE NAG C 501
15BC6SOFTWAREHIS C:85 , ASN C:229 , LYS C:231 , ASN C:241BINDING SITE FOR RESIDUE NAG C 502
16BC7SOFTWAREASN A:354 , ASN A:355 , SER A:464 , LYS C:252 , ASN C:262 , ARG C:379 , CYS C:445 , VAL C:446 , SER C:447 , NAG C:511 , HOH C:604 , HOH C:606 , HOH C:613 , HOH C:616BINDING SITE FOR RESIDUE NAG C 503
17BC8SOFTWAREASN C:276 , THR C:278 , ASN C:279BINDING SITE FOR RESIDUE NAG C 504
18BC9SOFTWAREGLU C:268 , GLU C:269 , ILE C:270 , ASN C:289BINDING SITE FOR RESIDUE NAG C 505
19CC1SOFTWAREASN C:295 , GLU C:332 , LYS C:442 , HOH C:675BINDING SITE FOR RESIDUE NAG C 506
20CC2SOFTWAREASN C:334 , THR C:336 , LYS C:337BINDING SITE FOR RESIDUE NAG C 507
21CC3SOFTWAREGLU C:351 , ASN C:354 , ASN C:355BINDING SITE FOR RESIDUE NAG C 508
22CC4SOFTWARETHR C:372 , ASN C:386 , THR C:388 , HOH C:622BINDING SITE FOR RESIDUE NAG C 509
23CC5SOFTWAREASN C:392 , CYS C:395BINDING SITE FOR RESIDUE NAG C 510
24CC6SOFTWARELYS A:350 , ASN A:355 , HOH A:625 , ASN C:262 , SER C:291 , ASN C:448 , NAG C:503 , HOH C:691BINDING SITE FOR RESIDUE NAG C 511
25CC7SOFTWARELEU C:52 , ALA C:73 , GLN C:103 , ASP C:107 , HOH C:620BINDING SITE FOR RESIDUE EPE C 512
26CC8SOFTWAREVAL C:255 , SER C:256 , GLU C:370 , SER C:375 , ASN C:425 , TRP C:427 , GLY C:473 , ASN C:474BINDING SITE FOR RESIDUE 0LM C 513

(-) SS Bonds  (14, 14)

Asymmetric Unit
No.Residues
1A:54 -A:74
2A:119 -A:205
3A:218 -A:247
4A:228 -A:239
5A:296 -A:331
6A:378 -A:445
7A:385 -A:418
8C:54 -C:74
9C:119 -C:205
10C:218 -C:247
11C:228 -C:239
12C:296 -C:331
13C:378 -C:445
14C:385 -C:418

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4DKO)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4DKO)

(-) 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 A from PDB  Type:PROTEIN  Length:339
 aligned with Q0ED31_9HIV1 | Q0ED31 from UniProtKB/TrEMBL  Length:857

    Alignment length:444
                                    52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482    
         Q0ED31_9HIV1    43 VWKDADTTLFCASDAKAHETEVHNVWATHACVPTDPNPQEIHLENVTENFNMWKNNMVEQMQEDVISLWDQSLQPCVKLTPLCVTLHCTTAKLTNVTNITNVPNIGNITDEVRNCSFNMTTEIRDKKQKVHALFYKLDIVQIEDKNDSSKYRLINCNTSVIKQACPKISFDPIPIHYCTPAGYVILKCNDKNFNGTGPCKNVSSVQCTHGIKPVVSTQLLLNGSLAEEEIIIRSENLTNNAKTIIVHLNKSVEINCTRPSNNMRTSMRIGPGQVFYRTGSITGDIRKAYCEINGTKWNKVLKQVTEKLKEHFNNKTIIFQPPSGGDLEITMHHFNCRGEFFYCNTTQLFNNTCIGNETMKGCNGTITLPCKIKQIINMWQGTGQAMYAPPIDGKINCVSNITGILLTRDGGANNTSNETFRPGGGNIKDNWRSELYKYKVVQIE 486
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eee.....eeee.......hhhhhhhhhhhee......eee.....eeee...hhhhhhhhhhhhhhhhhhh...eeee.----------------------------------------------------------------------------.eeee.............eee....eeeeee.......eeee..eeee.............eee.........eee..........eeeeeeeeeeeeeee...---------------------....eeeeeeehhhhhhhhhhhhhhhhhhh...eeee......hhhhhheeeee..eeeee...........--------..eeeeeeee..eee......eee........eeeeeeeeeeeeee........eeeeee....hhhhhhhhhh.eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4dko A  44 VWKDADTTLFCASDAKAHETEVHNVWATHACVPTDPNPQEIHLENVTENFNMWKNNMVEQMQEDVISLWDQSLQPCVKLTG----------------------------------------------------------------------------GSVIKQACPKISFDPIPIHYCTPAGYVILKCNDKNFNGTGPCKNVSSVQCTHGIKPVVSTQLLLNGSLAEEEIIIRSENLTNNAKTIIVHLNKSVEINCTRPSN---------------------GDIRKAYCEINGTKWNKVLKQVTEKLKEHFNNKTIIFQPPSGGDLEITMHSFNCRGEFFYCNTTQLFNNTCI--------NGTITLPCKIKQIINMWQGTGQAMYAPPIDGKINCVSNITGILLTRDGGANNTSNETFRPGGGNIKDNWRSELYKYKVVQIE 492
                                    53        63        73        83        93       103       113       123|        -         -         -         -         -         -         -       200       210       220       230       240       250       260       270       280       290       300|        -         -  |    331       341       351   ||  362       372       382       392   |     -  |    418       428       438       448       458       468       478       488    
                                                                                                          124                                                                          198                                                                                                    301                   324                            355|                                    396      411                                                                                 
                                                                                                                                                                                                                                                                                                                                                    357                                                                                                                                 


Chain C from PDB  Type:PROTEIN  Length:339
 aligned with Q0ED31_9HIV1 | Q0ED31 from UniProtKB/TrEMBL  Length:857

    Alignment length:444
                                    52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482    
         Q0ED31_9HIV1    43 VWKDADTTLFCASDAKAHETEVHNVWATHACVPTDPNPQEIHLENVTENFNMWKNNMVEQMQEDVISLWDQSLQPCVKLTPLCVTLHCTTAKLTNVTNITNVPNIGNITDEVRNCSFNMTTEIRDKKQKVHALFYKLDIVQIEDKNDSSKYRLINCNTSVIKQACPKISFDPIPIHYCTPAGYVILKCNDKNFNGTGPCKNVSSVQCTHGIKPVVSTQLLLNGSLAEEEIIIRSENLTNNAKTIIVHLNKSVEINCTRPSNNMRTSMRIGPGQVFYRTGSITGDIRKAYCEINGTKWNKVLKQVTEKLKEHFNNKTIIFQPPSGGDLEITMHHFNCRGEFFYCNTTQLFNNTCIGNETMKGCNGTITLPCKIKQIINMWQGTGQAMYAPPIDGKINCVSNITGILLTRDGGANNTSNETFRPGGGNIKDNWRSELYKYKVVQIE 486
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eee.....eeee.......hhhhhhhhhheee.......ee.....eeee...hhhhhhhhhhhhhhhhhhh...eeee.----------------------------------------------------------------------------.eeee.............eee....eeeeee.......eeee..eeee.............eee.........eee..........eeeeeeeeeeeeeee...---------------------....eeeeeeehhhhhhhhhhhhhhhhh......eee......hhhhhheeeee..eeeee.hhhhhh....--------..eeeeeeee..eee.....eeee........eeeeeeeeeeeeee.........eeeee....hhhhhhhhhh.eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4dko C  44 VWKDADTTLFCASDAKAHETEVHNVWATHACVPTDPNPQEIHLENVTENFNMWKNNMVEQMQEDVISLWDQSLQPCVKLTG----------------------------------------------------------------------------GSVIKQACPKISFDPIPIHYCTPAGYVILKCNDKNFNGTGPCKNVSSVQCTHGIKPVVSTQLLLNGSLAEEEIIIRSENLTNNAKTIIVHLNKSVEINCTRPSN---------------------GDIRKAYCEINGTKWNKVLKQVTEKLKEHFNNKTIIFQPPSGGDLEITMHSFNCRGEFFYCNTTQLFNNTCI--------NGTITLPCKIKQIINMWQGTGQAMYAPPIDGKINCVSNITGILLTRDGGANNTSNETFRPGGGNIKDNWRSELYKYKVVQIE 492
                                    53        63        73        83        93       103       113       123|        -         -         -         -         -         -         -       200       210       220       230       240       250       260       270       280       290       300|        -         -  |    331       341       351   ||  362       372       382       392   |     -  |    418       428       438       448       458       468       478       488    
                                                                                                          124                                                                          198                                                                                                    301                   324                            355|                                    396      411                                                                                 
                                                                                                                                                                                                                                                                                                                                                    357
   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  (0, 0)

(no "SCOP Domain" information available for 4DKO)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (14, 14)

Asymmetric Unit(hide GO term definitions)
Chain A,C   (Q0ED31_9HIV1 | Q0ED31)
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: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: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: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.

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 Related Entries

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

UniProtKB/TrEMBL
        Q0ED31_9HIV1 | Q0ED31: 3ngb 3se8 3se9 3tgt 3u7y 4dkp 4dkq 4dkr 4dku 4dkv 4dvs 4dvt 4dvv 4dvw 4dvx 4h8w 4i54 4jb9 4jdt 4jkp 4jpv 4jpw 4lsp 4lsq 4lsr 4lsu 4olu 4olv 4olw 4olx 4oly 4olz 4om0 4om1 4p9h 4rfn 4rfo 4rz8 4xnz 4xvt 4ydj 4ydk 4ydl 4yfl

(-) Related Entries Specified in the PDB File

4dkp 4dkq 4dkr