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(-) Description

Title :  HIV-1 GP120 COMPLEX WITH BNM-III-170
 
Authors :  S. Liang, W. A. Hendrickson
Date :  03 Dec 15  (Deposition) - 30 Mar 16  (Release) - 30 Mar 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym./Biol. Unit :  A,D
Keywords :  Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. Melillo, S. Liang, J. Park, A. Schon, J. R. Courter, J. M. Lalonde, D. J. Wendler, A. M. Princiotto, M. S. Seaman, E. Freire, J. Sodroski, N. Madani, W. A. Hendrickson, A. B. Smith
Small-Molecule Cd4-Mimics: Structure-Based Optimization Of Hiv-1 Entry Inhibition.
Acs Med. Chem. Lett. V. 7 330 2016
PubMed-ID: 26985324  |  Reference-DOI: 10.1021/ACSMEDCHEMLETT.5B00471

(-) Compounds

Molecule 1 - ENVELOPE GLYCOPROTEIN GP120 OF HIV-1 CLADE C
    Chains: D, A
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK 293 GNTI- CELLS
    Expression System Taxid: 9606
    Organism Scientific: HUMAN IMMUNODEFICIENCY VIRUS 1
    Organism Taxid: 11676

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 14)

Asymmetric/Biological Unit (2, 14)
No.NameCountTypeFull Name
15VG2Ligand/Ion~{N}'-[(1~{R},2~{R})-2-(CARBAMIMIDAMIDOMETHYL)-5-(METHYLAMINOMETHYL)-2,3-DIHYDRO-1~{H}-INDEN-1-YL]-~{N}-(4-CHLORANYL-3-FLUORANYL-PHENYL)ETHANEDIAMIDE
2NAG12Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN D:234binding site for residue NAG D 501
02AC2SOFTWARELYS A:59 , ASP D:211 , ASN D:262 , ASN D:446 , SER D:447binding site for residue NAG D 502
03AC3SOFTWAREGLU A:275 , LYS A:282 , NAG A:504 , ASN D:276 , THR D:278 , ASN D:279binding site for residue NAG D 503
04AC4SOFTWAREGLU D:268 , GLU D:269 , ASN D:289 , LYS D:344binding site for residue NAG D 504
05AC5SOFTWARETHR D:372 , ASN D:386 , SER D:388binding site for residue NAG D 505
06AC6SOFTWAREPRO D:363 , ASP D:389 , ASN D:392 , THR D:406 , ARG D:408binding site for residue NAG D 506
07AC7SOFTWAREVAL D:255 , GLU D:370 , ILE D:371 , SER D:375 , PHE D:376 , ASN D:377 , ILE D:424 , ASN D:425 , MET D:426 , TRP D:427 , GLU D:429 , VAL D:430 , GLY D:431 , GLY D:472 , GLY D:473 , MET D:475binding site for residue 5VG D 507
08AC8SOFTWARESER A:256 , GLU A:370 , ILE A:371 , SER A:375 , PHE A:376 , ASN A:377 , ASN A:425 , MET A:426 , TRP A:427 , GLU A:429 , VAL A:430 , GLY A:431 , GLY A:473 , MET A:475binding site for residue 5VG A 501
09AC9SOFTWAREASN A:234 , HIS A:352binding site for residue NAG A 502
10AD1SOFTWAREASN A:262 , CYS A:445 , ASN A:446 , SER A:447binding site for residue NAG A 503
11AD2SOFTWAREASN A:276 , THR D:278 , NAG D:503binding site for residue NAG A 504
12AD3SOFTWAREGLU A:268 , GLU A:269 , ASN A:289 , LYS A:344binding site for residue NAG A 505
13AD4SOFTWARETHR A:372 , ASN A:386 , SER A:388binding site for residue NAG A 506
14AD5SOFTWAREASP A:389 , ASN A:392 , ARG A:396binding site for residue NAG A 507

(-) SS Bonds  (14, 14)

Asymmetric/Biological 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
8D:54 -D:74
9D:119 -D:205
10D:218 -D:247
11D:228 -D:239
12D:296 -D:331
13D:378 -D:445
14D:385 -D:418

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5F4P)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5F4P)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5F4P)

(-) Exons   (0, 0)

(no "Exon" information available for 5F4P)

(-) 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:335
                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee.......hhhhhhhhhhhee..............eeee...hhhhhhhhhhhhhhhhhhh...eeee..eeee.............eee.....eeeee.......eeee..eeee.............eee.........eeee.........eeeeeeeeeeeeeee.....eeeeeeehhhhhhhhhhhhhhhhhhh...eeee......hhhhhheeeee..eeeee.......eeee..eeee.......eeeeeeee..eee......eee........eeeeeeeeeeeeee..eeeeee....hhhhhhh....eeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5f4p A  49 KTTLFCASDAKAYEKEVHNVWATHACVPTDPNPQEMVLANVTENFNMWKNDMVEQMHEDIISLWDESLKPCVKLTGGSAITQACPKVSFDPIPLHYCAPAGFAILKCNNKTFNGTGPCRNVSTVQCTHGIKPVVSTQLLLNGSLAEEEIIIRSENLTNNAKTIIVHLNESVNIVCTRPNNIRQAHCNINESKWNNTLQKVGEELAKHFPSKTIKFEPSSGGDLEITTHSFNCRGEFFYCNTSDLFNGTYRNGTYNHTGRSSNGTITLQCKIKQIINMWQEVGRAIYAPPIEGEITCNSNITGLLLLRDDTETFRPGGGDMRDNWRSELYKYKVVE 490
                                    58        68        78        88        98       108       118     ||201       211       221       231       241       251       261       271       281       291       325       335       345       356       366       376       386       396  ||   409       419       429       439       449       465       475       485     
                                                                                                     124|                                                                                                   300|                          354|                                        399|                                                   457|                          
                                                                                                      198                                                                                                    325                           356                                         403                                                    464                          


Chain D from PDB  Type:PROTEIN  Length:335
                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee.......hhhhhhhhhhhee..............eeee...hhhhhhhhhhhhhhhhhhh...eeee..eeee.............eee.....eeeee.......eeee..eeee.............eee.........eee..........eeeeeeeeeeeeeee.....eeeeeeehhhhhhhhhhhhhhhhhh....eeee......hhhhhheeeee..eeeee.......eeee..eeee.......eeeeeeeee.eee......eee........eeeeeeeeeeeeee..eeeeee...hhhhhhhh.....eee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5f4p D  49 KTTLFCASDAKAYEKEVHNVWATHACVPTDPNPQEMVLANVTENFNMWKNDMVEQMHEDIISLWDESLKPCVKLTGGSAITQACPKVSFDPIPLHYCAPAGFAILKCNNKTFNGTGPCRNVSTVQCTHGIKPVVSTQLLLNGSLAEEEIIIRSENLTNNAKTIIVHLNESVNIVCTRPNNIRQAHCNINESKWNNTLQKVGEELAKHFPSKTIKFEPSSGGDLEITTHSFNCRGEFFYCNTSDLFNGTYRNGTYNHTGRSSNGTITLQCKIKQIINMWQEVGRAIYAPPIEGEITCNSNITGLLLLRDDTETFRPGGGDMRDNWRSELYKYKVVE 490
                                    58        68        78        88        98       108       118     ||201       211       221       231       241       251       261       271       281       291       325       335       345       356       366       376       386       396  ||   409       419       429       439       449       465       475       485     
                                                                                                     124|                                                                                                   300|                          354|                                        399|                                                   457|                          
                                                                                                      198                                                                                                    325                           356                                         403                                                    464
   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 5F4P)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5F4P)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5F4P)

(-) Gene Ontology  (14, 14)

Asymmetric/Biological Unit(hide GO term definitions)

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        C6G099_9HIV1 | C6G099: 3tgr 3tgs 4i53 4lsv 5f4l 5f4r 5f4u

(-) Related Entries Specified in the PDB File

5f4l 5f4r 5f4u