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 :  ARTIFICIAL HIV FUSION INHIBITOR AP1 FUSED TO THE C-TERMINUS OF GP41 NHR
 
Authors :  Y. Zhu, S. Ye, R. Zhang
Date :  17 Jul 15  (Deposition) - 16 Sep 15  (Release) - 16 Sep 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.11
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Enfuvirtide, Hiv Fusion Inhibitor, Ap1, Gp41, 6-Hb, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  X. Zhu, Y. Zhu, S. Ye, Q. Wang, W. Xu, S. Su, Z. Sun, F. Yu, Q. Liu, C. Wang, T. Zhang, Z. Zhang, X. Zhang, J. Xu, L. Du, K. Liu, L. Lu, R. Zhang, S. Jian
Improved Pharmacological And Structural Properties Of Hiv Fusion Inhibitor Ap3 Over Enfuvirtide: Highlighting Advantages Of Artificial Peptide Strategy.
Sci Rep V. 5 13028 2015
PubMed-ID: 26286358  |  Reference-DOI: 10.1038/SREP13028

(-) Compounds

Molecule 1 - ENVELOPE GLYCOPROTEIN,AP1
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: C-TERMINUS (UNP RESIDUES 35-70)
    Gene: ENV
    Organism Scientific: HUMAN IMMUNODEFICIENCY VIRUS 1, SYNTHETIC CONSTRUCT
    Organism Taxid: 11676, 32630
    Other Details: THE FUSION PROTEIN OF EXPRESSION TAG, C-TERMINUS RESIDUES 35-70 FROM GP4 AND ARTIFICIAL INHIBITOR AP1

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 5)

Asymmetric/Biological Unit (1, 5)
No.NameCountTypeFull Name
1GOL5Ligand/IonGLYCEROL

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:42 , TRP A:46 , GLU A:49 , LEU C:23 , TRP C:26binding site for residue GOL A 101
2AC2SOFTWAREGLY B:39 , ARG B:40 , GLY B:41 , GLY B:42 , TRP B:43 , MET B:44 , GLU B:45binding site for residue GOL B 101
3AC3SOFTWAREGLN B:30 , ARG B:34 , LEU C:36 , GLY C:41 , TRP C:43binding site for residue GOL B 102
4AC4SOFTWARELYS C:62 , LYS C:63 , GLU C:66 , HOH C:202 , HOH C:214binding site for residue GOL C 101
5AC5SOFTWARELYS C:29 , GLN C:32 , ASP C:47 , HOH C:213binding site for residue GOL C 102

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5CMU)

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5CMU)

(-) 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:73
                                                                                                        
               SCOP domains ------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------- Transcript
                  5cmu A  0 SSGIVQQQNNLLRAIEAQQHLLQLTVWGIKQLQARILSGGRGGWMEWDREIEELIKKSEELIKKIEEQIKKQE 72
                                     9        19        29        39        49        59        69   


Chain B from PDB  Type:PROTEIN  Length:72
                                                                                                       
               SCOP domains ------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------ Transcript
                  5cmu B  1 SGIVQQQNNLLRAIEAQQHLLQLTVWGIKQLQARILSGGRGGWMEWDREIEELIKKSEELIKKIEEQIKKQE 72
                                    10        20        30        40        50        60        70  


Chain C from PDB  Type:PROTEIN  Length:72
                                                                                                       
               SCOP domains ------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------ Transcript
                  5cmu C  1 SGIVQQQNNLLRAIEAQQHLLQLTVWGIKQLQARILSGGRGGWMEWDREIEELIKKSEELIKKIEEQIKKQE 72
                                    10        20        30        40        50        60        70
   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 5CMU)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (32, 34)

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
    GOL  [ 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 ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 5cmu)
 

(-) 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
  5cmu
    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
  ENV_HV1H2 | P04578
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  Q1HMR5_9HIV1 | Q1HMR5
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
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
  ENV_HV1H2 | P04578
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  Q1HMR5_9HIV1 | Q1HMR5
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        ENV_HV1H2 | P04578: 1aik 1df4 1df5 1dlb 1g9m 1gc1 1gzl 1k33 1k34 1mzi 1opn 1opt 1opw 1rzj 2cmr 2me1 2mg1 2mg2 2mg3 2ny7 2pv6 2x7r 2xra 2zzo 3d0v 3dnl 3dnn 3dno 3dro 3idx 3idy 3j70 3tyg 3vie 4jpj 4jpk 4ydv 4zto 5bn0 5c0r 5c0s 5cil 5cin 5cmz 5cn0 5dd0 5ghw 5h0n 5hfl 5hm1 5ivx 5ka5 5ka6 5x08
        Q1HMR5_9HIV1 | Q1HMR5: 5bn0 5cmz 5cn0

(-) Related Entries Specified in the PDB File

5cmz 5cn0