Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  HIV-1 GP120 COMPLEX WITH BNW-IV-147
 
Authors :  S. Liang, W. A. Hendrickson
Date :  03 Dec 15  (Deposition) - 30 Mar 16  (Release) - 30 Mar 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym./Biol. Unit :  A,C
Keywords :  Gp120, 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: A, C
    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 : AC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 16)

Asymmetric/Biological Unit (3, 16)
No.NameCountTypeFull Name
15VF2Ligand/Ion~{N}'-[(1~{R},2~{R})-2-(CARBAMIMIDAMIDOMETHYL)-5-[[CARBAMIMIDOYL(METHYL)AMINO]METHYL]-2,3-DIHYDRO-1~{H}-INDEN-1-YL]-~{N}-(4-CHLORANYL-3-FLUORANYL-PHENYL)ETHANEDIAMIDE
2FMT2Ligand/IonFORMIC ACID
3NAG12Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (16, 16)

Asymmetric Unit (16, 16)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:425 , ARG A:432 , 5VF A:508binding site for residue FMT A 501
02AC2SOFTWAREASN A:234 , THR A:236 , PRO A:238 , LEU A:277binding site for residue NAG A 502
03AC3SOFTWAREASP A:211 , LYS A:252 , ASN A:262 , CYS A:445 , ASN A:446 , SER A:447binding site for residue NAG A 503
04AC4SOFTWAREASN A:276 , THR A:278 , HOH A:603 , LYS C:97 , GLU C:275 , LYS C:282 , NAG C:504binding site for residue NAG A 504
05AC5SOFTWAREGLU A:268 , GLU A:269 , ILE A:270 , ASN A:289binding site for residue NAG A 505
06AC6SOFTWAREASN A:386 , SER A:388binding site for residue NAG A 506
07AC7SOFTWAREASN A:392 , THR A:406 , ARG A:408binding site for residue NAG A 507
08AC8SOFTWARESER A:256 , THR A:257 , GLU A:370 , ILE A:371 , SER A:375 , PHE A:376 , ASN A:377 , PHE A:382 , ASN A:425 , MET A:426 , TRP A:427 , GLU A:429 , VAL A:430 , GLY A:431 , GLY A:473 , MET A:475 , FMT A:501binding site for residue 5VF A 508
09AC9SOFTWAREASN C:425 , GLY C:431 , ARG C:432 , 5VF C:508binding site for residue FMT C 501
10AD1SOFTWAREASN C:234 , THR C:236 , LEU C:277 , HIS C:352binding site for residue NAG C 502
11AD2SOFTWAREASP C:211 , LYS C:252 , ASN C:262 , CYS C:445 , ASN C:446 , SER C:447binding site for residue NAG C 503
12AD3SOFTWARETHR A:278 , NAG A:504 , ASN C:276 , THR C:278binding site for residue NAG C 504
13AD4SOFTWAREGLU C:268 , GLU C:269 , ILE C:270 , ASN C:289 , GLU C:348binding site for residue NAG C 505
14AD5SOFTWARETHR C:372 , ASN C:386 , SER C:388binding site for residue NAG C 506
15AD6SOFTWAREPRO C:363 , ASN C:392 , ARG C:396 , ASN C:404binding site for residue NAG C 507
16AD7SOFTWARESER C:256 , GLU C:370 , ILE C:371 , SER C:375 , PHE C:376 , ASN C:377 , PHE C:382 , ASN C:425 , MET C:426 , TRP C:427 , GLU C:429 , VAL C:430 , GLY C:431 , GLY C:473 , MET C:475 , FMT C:501binding site for residue 5VF C 508

(-) SS Bonds  (13, 13)

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
8C:54 -C:74
9C:218 -C:247
10C:228 -C:239
11C:296 -C:331
12C:378 -C:445
13C:385 -C:418

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5F4R)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5F4R)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5F4R)

(-) Exons   (0, 0)

(no "Exon" information available for 5F4R)

(-) 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......................eeeeeeeeeeeeee..eeeeee......hhhhhhhh.eeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5f4r 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 C from PDB  Type:PROTEIN  Length:335
                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee.......hhhhhhhhhhhee.......ee.....eeee...hhhhhhhhhhhhhhhhhhh...eeee..eeee.............eee.....eeeee.......eeee..eeee.............eee.........eee..........eeeeeeeeeeeeeee.....eeeeeeehhhhhhhhhhhhhhhhhhh...eeee......hhhhhheeeee..eeeee.......eeee..eeee.......eeeeeeee......................eeeeeeeeeeeeee..eeeeee......hhhhhhhh.eeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5f4r C  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 5F4R)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5F4R)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5F4R)

(-) Gene Ontology  (14, 14)

Asymmetric/Biological Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    5VF  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    FMT  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NAG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    AD1  [ RasMol ]  +environment [ RasMol ]
    AD2  [ RasMol ]  +environment [ RasMol ]
    AD3  [ RasMol ]  +environment [ RasMol ]
    AD4  [ RasMol ]  +environment [ RasMol ]
    AD5  [ RasMol ]  +environment [ RasMol ]
    AD6  [ RasMol ]  +environment [ RasMol ]
    AD7  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 5f4r)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  5f4r
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  C6G099_9HIV1 | C6G099
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  C6G099_9HIV1 | C6G099
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        C6G099_9HIV1 | C6G099: 3tgr 3tgs 4i53 4lsv 5f4l 5f4p 5f4u

(-) Related Entries Specified in the PDB File

5f4l 5f4p 5f4u