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 :  CRYSTAL STRUCTURE OF THE GP2 CORE DOMAIN FROM THE CALIFORNIA ACADEMY OF SCIENCE VIRUS
 
Authors :  V. N. Malashkevich, J. F. Koellhoffer, Z. Dai, R. Toro, J. R. Lai, S. C. Al York Structural Genomics Research Consortium (Nysgrc)
Date :  04 Oct 13  (Deposition) - 27 Nov 13  (Release) - 02 Apr 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.99
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B,C  (1x)
Biol. Unit 2:  D,E,F  (1x)
Keywords :  Cas Virus, Post-Fusion Conformation, Structural Genomics, Psi- Biology, New York Structural Genomics Research Consortium, Nysgrc, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. F. Koellhoffer, Z. Dai, V. N. Malashkevich, M. D. Stenglein, Y. Liu, R. Toro, J. S Harrison, K. Chandran, J. L. Derisi, S. C. Almo, J. R. Lai
Structural Characterization Of The Glycoprotein Gp2 Core Domain From The Cas Virus, A Novel Arenavirus-Like Species.
J. Mol. Biol. V. 426 1452 2014
PubMed-ID: 24333483  |  Reference-DOI: 10.1016/J.JMB.2013.12.009

(-) Compounds

Molecule 1 - GP2 ECTODOMAIN
    ChainsA, B, C, D, E, F
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET22B
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneGP2
    Organism ScientificCAS VIRUS
    Organism Taxid1223561

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit ABCDEF
Biological Unit 1 (1x)ABC   
Biological Unit 2 (1x)   DEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 11)

Asymmetric Unit (1, 11)
No.NameCountTypeFull Name
1MPD11Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
Biological Unit 1 (1, 7)
No.NameCountTypeFull Name
1MPD7Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
Biological Unit 2 (1, 4)
No.NameCountTypeFull Name
1MPD4Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:277 , MET A:345 , HOH A:531 , ASN E:277 , HIS E:342 , LYS E:346BINDING SITE FOR RESIDUE MPD A 401
02AC2SOFTWARESER A:270 , ASN E:281 , HOH E:508BINDING SITE FOR RESIDUE MPD A 402
03AC3SOFTWARETHR A:279 , ILE B:272 , ALA B:276 , THR B:279 , THR C:279BINDING SITE FOR RESIDUE MPD B 401
04AC4SOFTWARELYS A:340 , LYS B:274 , TYR B:278 , LYS D:274 , TYR D:278 , LYS F:340BINDING SITE FOR RESIDUE MPD B 402
05AC5SOFTWAREASN B:281 , PHE B:284 , HOH B:536 , SER D:270BINDING SITE FOR RESIDUE MPD B 403
06AC6SOFTWAREMET C:345 , LYS C:346 , HOH C:505 , HIS F:342 , LYS F:346BINDING SITE FOR RESIDUE MPD C 401
07AC7SOFTWARELYS B:340 , LYS C:274 , TYR C:278 , LYS E:340 , TYR F:278 , HOH F:409BINDING SITE FOR RESIDUE MPD C 402
08AC8SOFTWARETHR D:279 , ALA E:276 , THR E:279 , ALA F:276 , THR F:279BINDING SITE FOR RESIDUE MPD D 401
09AC9SOFTWAREASN B:277 , LYS B:346 , ASN D:277 , HIS D:342BINDING SITE FOR RESIDUE MPD D 402
10BC1SOFTWARETYR A:278 , LYS C:340 , LYS D:340 , LYS E:274 , TYR E:278 , HOH E:530BINDING SITE FOR RESIDUE MPD E 401
11BC2SOFTWAREASN A:281 , SER E:270 , HOH E:532BINDING SITE FOR RESIDUE MPD E 402

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1E:315 -E:323

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4N21)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4N21)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4N21)

(-) Exons   (0, 0)

(no "Exon" information available for 4N21)

(-) 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:123
                                                                                                                                                           
               SCOP domains d4n21a_ A: automated matches                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------- Transcript
                 4n21 A 229 ENLYFQGNMKQIEDKIEEILSKIYHIENEIARIKKLIGAIASKIIKTANYTTNALFLLNKEESEIRDHVVEHELALNYLLAHQGGLCNVVKGPMCSSDIDDFSKNVSDMIDKVHEEMKKFYHE 351
                                   238       248       258       268       278       288       298       308       318       328       338       348   

Chain B from PDB  Type:PROTEIN  Length:123
                                                                                                                                                           
               SCOP domains d4n21b_ B: automated matches                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------- Transcript
                 4n21 B 229 ENLYFQGNMKQIEDKIEEILSKIYHIENEIARIKKLIGAIASKIIKTANYTTNALFLLNKEESEIRDHVVEHELALNYLLAHQGGLCNVVKGPMCSSDIDDFSKNVSDMIDKVHEEMKKFYHE 351
                                   238       248       258       268       278       288       298       308       318       328       338       348   

Chain C from PDB  Type:PROTEIN  Length:124
                                                                                                                                                            
               SCOP domains d4n21c_ C: automated matches                                                                                                 SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------- Transcript
                 4n21 C 228 HENLYFQGNMKQIEDKIEEILSKIYHIENEIARIKKLIGAIASKIIKTANYTTNALFLLNKEESEIRDHVVEHELALNYLLAHQGGLCNVVKGPMCSSDIDDFSKNVSDMIDKVHEEMKKFYHE 351
                                   237       247       257       267       277       287       297       307       317       327       337       347    

Chain D from PDB  Type:PROTEIN  Length:123
                                                                                                                                                           
               SCOP domains d4n21d_ D: automated matches                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhh...........hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------- Transcript
                 4n21 D 229 ENLYFQGNMKQIEDKIEEILSKIYHIENEIARIKKLIGAIASKIIKTANYTTNALFLLNKEESEIRDHVVEHELALNYLLAHQGGLCNVVKGPMCSSDIDDFSKNVSDMIDKVHEEMKKFYHE 351
                                   238       248       258       268       278       288       298       308       318       328       338       348   

Chain E from PDB  Type:PROTEIN  Length:121
                                                                                                                                                         
               SCOP domains d4n21e_ E: automated matches                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 4n21 E 230 NLYFQGNMKQIEDKIEEILSKIYHIENEIARIKKLIGAIASKIIKTANYTTNALFLLNKEESEIRDHVVEHELALNYLLAHQGGLCNVVKGPMCSSDIDDFSKNVSDMIDKVHEEMKKFYH 350
                                   239       249       259       269       279       289       299       309       319       329       339       349 

Chain F from PDB  Type:PROTEIN  Length:124
                                                                                                                                                            
               SCOP domains d4n21f_ F: automated matches                                                                                                 SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------- Transcript
                 4n21 F 228 HENLYFQGNMKQIEDKIEEILSKIYHIENEIARIKKLIGAIASKIIKTANYTTNALFLLNKEESEIRDHVVEHELALNYLLAHQGGLCNVVKGPMCSSDIDDFSKNVSDMIDKVHEEMKKFYHE 351
                                   237       247       257       267       277       287       297       307       317       327       337       347    

   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, 6)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4N21)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4N21)

(-) Gene Ontology  (2, 2)

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
    MPD  [ 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 ]
    BC1  [ RasMol ]  +environment [ RasMol ]
    BC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4n21)
 
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
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  4n21
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  J7H5L9_9VIRU | J7H5L9
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  J7H5L9_9VIRU | J7H5L9
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        J7H5L9_9VIRU | J7H5L94n23

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4N21)