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 :  RE-REFINEMENT OF CAP-1 HIV-CA COMPLEX
 
Authors :  P. T. Lang, J. M. Holton, J. S. Fraser, T. Alber
Date :  08 Dec 13  (Deposition) - 26 Feb 14  (Release) - 26 Feb 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym./Biol. Unit :  C
Keywords :  Capsid, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. T. Lang, J. M. Holton, J. S. Fraser, T. Alber
Protein Structural Ensembles Are Revealed By Redefining X-Ray Electron Density Noise.
Proc. Natl. Acad. Sci. Usa V. 111 237 2014
PubMed-ID: 24363322  |  Reference-DOI: 10.1073/PNAS.1302823110

(-) Compounds

Molecule 1 - GAG-POL POLYPROTEIN
    Chains: C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: HIV-1 CAPSID (UNP RESIDUES 133-278)
    Organism Common: HIV-1
    Organism Scientific: HUMAN IMMUNODEFICIENCY VIRUS TYPE 1
    Organism Taxid: 11698
    Strain: NEW YORK-5 ISOLATE
    Synonym: CAPSID PROTEIN P24

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric/Biological Unit (3, 4)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2JPR1Ligand/Ion1-(3-CHLORO-4-METHYLPHENYL)-3-{2-[({5-[(DIMETHYLAMINO)METHYL]-2-FURYL}METHYL)THIO]ETHYL}UREA
3ZN2Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN C:50 , LEU C:111 , HOH C:363BINDING SITE FOR RESIDUE CL C 201
2AC2SOFTWAREHIS C:84 , HIS C:87 , GLU C:98 , HOH C:385BINDING SITE FOR RESIDUE ZN C 202
3AC3SOFTWAREHIS C:120BINDING SITE FOR RESIDUE ZN C 203
4AC4SOFTWAREVAL C:27 , ALA C:31 , PHE C:32 , ASN C:57 , THR C:58 , VAL C:59 , GLY C:60 , GLY C:61 , HIS C:62 , MET C:66 , ARG C:132 , LEU C:136 , LEU C:138 , ASN C:139 , ILE C:141 , HOH C:335 , HOH C:338 , HOH C:433 , HOH C:434 , HOH C:435BINDING SITE FOR RESIDUE JPR C 204

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4NX4)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Asn C:121 -Pro C:122

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4NX4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4NX4)

(-) Exons   (0, 0)

(no "Exon" information available for 4NX4)

(-) 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 C from PDB  Type:PROTEIN  Length:145
                                                                                                                                                                                 
               SCOP domains d4nx4c_ C: HIV-1 capsid protein                                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee.....eee...hhhhhhhhhhhhhhhh...hhhhhhhhh....hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh...............hhhhhh....hhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4nx4 C   1 PIVQNLQGQMVHQAISPRTLNAWVKVVEEKAFSPEVIPMFSALSEGATPQDLNTMLNTVGGHQAAMQMLKETINEEAAEWDRLHPVHAGPIAPGQMREPRGSDIAGTTSTLQEQIGWMTHNPPIPVGEIYKRWIILGLNKIVRMY 145
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140
   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  (1, 1)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4NX4)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4NX4)

(-) Gene Ontology  (48, 48)

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
    CL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    JPR  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ZN  [ 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
    Asn C:121 - Pro C:122   [ RasMol ]  
 

(-) 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
  4nx4
    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
  POL_HV1N5 | P12497
    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
  POL_HV1N5 | P12497
    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
        POL_HV1N5 | P12497: 1a43 1a8o 1afv 1ak4 1aum 1b92 1b9d 1b9f 1baj 1bhl 1bi4 1bis 1biu 1biz 1bl3 1gwp 1hiw 1hyv 1hyz 1itg 1k6y 1m9d 1qs4 1uph 1wjb 1wjd 1wkn 1za9 2b4j 2gol 2gon 2h3f 2h3i 2h3q 2h3v 2h3z 2hmx 2hvp 2itg 2jpr 2jyg 2jyl 2lf4 2lya 2lyb 2m3z 2m8l 2m8n 2m8p 2ont 2pwm 2pwo 2pxr 2x2d 2xde 2xv6 2xxm 3av9 3ava 3avb 3avc 3avf 3avg 3avh 3avi 3avj 3avk 3avl 3avm 3avn 3dik 3dph 3ds0 3ds1 3ds2 3ds3 3ds4 3ds5 3dtj 3gv2 3h47 3h4e 3l3u 3l3v 3lpt 3lpu 3lry 3mge 3nf6 3nf7 3nf8 3nf9 3nfa 3p05 3p0a 3s85 3wne 3wnf 3wng 3wnh 4ah9 4ahr 4ahs 4aht 4ahu 4ahv 4coc 4cop 4dga 4dge 4dmn 4e1m 4e1n 4e91 4e92 4gvm 4gw6 4id1 4ipy 4jlh 4jmu 4lqw 4o0j 4o55 4o5b 4phv 4qnb 4wym 4zhr 5hvp 9hvp

(-) Related Entries Specified in the PDB File

2jpr NMR DETERMINATION OF COMPLEX
2pxr CRYSTAL STRUCTURE OF HIV-1 CA146 IN THE PRESENCE OF CAP-1. THIS ENTRY 4NX4 REFLECTS AN ALTERNATIVE MODELING OF X-RAY DATA R2PXRSF