Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  ARTIFICIAL HIV FUSION INHIBITOR AP3 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 :  2.57
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (3x)
Biol. Unit 2:  C,D  (3x)
Keywords :  Enfuvirtide, Hiv Fusion Inhibitor, Ap3, Gp41, 6-Hb, Viral Protein- Inhibitor Complex (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
    Chains: A, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 35-79
    Gene: ENV
    Organism Common: HIV1
    Organism Scientific: HUMAN IMMUNODEFICIENCY VIRUS 1
    Organism Taxid: 11676
    Synonym: GO41
 
Molecule 2 - ARTIFICIAL HIV ENTRY INHIBITOR AP3
    Chains: B, D
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (3x): AB  
Biological Unit 2 (3x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 7)

Asymmetric Unit (5, 7)
No.NameCountTypeFull Name
1ACE2Mod. Amino AcidACETYL GROUP
2EDO1Ligand/Ion1,2-ETHANEDIOL
3NH22Mod. Amino AcidAMINO GROUP
4P4G1Ligand/Ion1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE
5SO41Ligand/IonSULFATE ION
Biological Unit 1 (5, 15)
No.NameCountTypeFull Name
1ACE3Mod. Amino AcidACETYL GROUP
2EDO3Ligand/Ion1,2-ETHANEDIOL
3NH23Mod. Amino AcidAMINO GROUP
4P4G3Ligand/Ion1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE
5SO43Ligand/IonSULFATE ION
Biological Unit 2 (2, 6)
No.NameCountTypeFull Name
1ACE3Mod. Amino AcidACETYL GROUP
2EDO-1Ligand/Ion1,2-ETHANEDIOL
3NH23Mod. Amino AcidAMINO GROUP
4P4G-1Ligand/Ion1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE
5SO4-1Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:40 , LYS A:43 , HOH A:301 , HOH A:304 , ARG C:40 , LYS C:43binding site for residue SO4 A 201
2AC2SOFTWAREALA A:37 , ASP A:44 , HOH A:310binding site for residue EDO A 202
3AC3SOFTWARETYR C:41 , LEU C:42 , LYS C:43 , ASP C:44binding site for Di-peptide GLN C 45 and NH2 C 100
4AC4SOFTWARETRP C:26 , THR D:42 , GLU D:45 , TRP D:46 , LYS D:49binding site for Di-peptide ACE D 40 and MET D 41

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5CMZ)

(-) 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:44
                                                                            
               SCOP domains -------------------------------------------- SCOP domains
               CATH domains -------------------------------------------- CATH domains
               Pfam domains -------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------- PROSITE
                 Transcript -------------------------------------------- Transcript
                 5cmz A   3 IVQQQNNLLRAIEAQQHLLQLTVWGIKQLQARILAVERYLKDQx 100
                                    12        22        32        42  ||
                                                                     45|
                                                                     100-NH2


Chain B from PDB  Type:PROTEIN  Length:33
                                                                 
               SCOP domains --------------------------------- SCOP domains
               CATH domains --------------------------------- CATH domains
               Pfam domains --------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------- PROSITE
                 Transcript --------------------------------- Transcript
                 5cmz B  40 xMTWEEWDKKIEELIKKSEELIKKIEEQIKKQE  72
                            |       49        59        69   
                            |                                
                           40-ACE                            


Chain C from PDB  Type:PROTEIN  Length:46
                                                                              
               SCOP domains ---------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------- PROSITE
                 Transcript ---------------------------------------------- Transcript
                 5cmz C   1 SGIVQQQNNLLRAIEAQQHLLQLTVWGIKQLQARILAVERYLKDQx 100
                                    10        20        30        40    ||
                                                                       45|
                                                                       100-NH2


Chain D from PDB  Type:PROTEIN  Length:35
                                                                   
               SCOP domains ----------------------------------- SCOP domains
               CATH domains ----------------------------------- CATH domains
               Pfam domains ----------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------- PROSITE
                 Transcript ----------------------------------- Transcript
                 5cmz D  40 xMTWEEWDKKIEELIKKSEELIKKIEEQIKKQEES  74
                            |       49        59        69     
                            |                                  
                           40-ACE
   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 5CMZ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (32, 34)

Asymmetric Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric 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
    ACE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    EDO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NH2  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    P4G  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 5cmz)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format | Biol. Unit 2 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
  5cmz
    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 5cmu 5cn0 5dd0 5ghw 5h0n 5hfl 5hm1 5ivx 5ka5 5ka6 5x08
        Q1HMR5_9HIV1 | Q1HMR5: 5bn0 5cmu 5cn0

(-) Related Entries Specified in the PDB File

5cmu 5cn0