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 :  CRYSTAL STRUCTURE OF HUMAN HISRS
 
Authors :  Z. Wei, J. Wu, J. J. Zhou, X. -L. Yang, M. Zhang, P. Schimmel
Date :  21 Jul 12  (Deposition) - 26 Sep 12  (Release) - 26 Sep 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Synthetase, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Z. Xu, Z. Wei, J. J. Zhou, F. Ye, W. S. Lo, F. Wang, C. F. Lau, J. Wu, L. A. Nangle, K. P. Chiang, X. L. Yang, M. Zhang, P. Schimmel
Internally Deleted Human Trna Synthetase Suggests Evolutionary Pressure For Repurposing.
Structure V. 20 1470 2012
PubMed-ID: 22958643  |  Reference-DOI: 10.1016/J.STR.2012.08.001

(-) Compounds

Molecule 1 - HISTIDINE--TRNA LIGASE, CYTOPLASMIC
    Chains: A, B
    EC Number: 6.1.1.21
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET32M
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 54-506
    Gene: HARS, HRS
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: HISTIDYL-TRNA SYNTHETASE, HISRS

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2IMD3Ligand/IonIMIDAZOLE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:132 , ASP A:175 , ASP A:177 , TYR A:331 , GLY A:360 , TYR A:363 , GLY A:381 , LEU A:382 , SER A:383BINDING SITE FOR RESIDUE IMD A 1001
2AC2SOFTWARETHR B:132 , ASP B:175 , ASP B:177 , TYR B:331 , TYR B:363 , GLY B:381 , LEU B:382 , SER B:383BINDING SITE FOR RESIDUE IMD B 1001
3AC3SOFTWAREGLU B:47 , ARG B:51 , PHE B:54 , GLU B:423BINDING SITE FOR RESIDUE IMD B 1002
4AC4SOFTWAREARG A:479 , ARG A:484 , ARG B:479 , ARG B:484BINDING SITE FOR RESIDUE CL B 1003

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4G84)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4G84)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4G84)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4G84)

(-) Exons   (0, 0)

(no "Exon" information available for 4G84)

(-) 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:433
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhhhhhhhhhhhhhhhhhhhhh..ee.....eeehhhhh................eee...hhhhhhhhhhhh....eeeeeeeeee.......eeeeeeeeee.....hhhhhhhhhhhhhhhhhhh...eeeeeeehhhhhhhhhhhh.hhhhhhhhhhhhhhhhh.hhhhhhhhhhhh...hhhhhhhhhhhhh.eehhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhh.eeee............eeeeeeeee..eeeeeeeeeee...hhhhh........eeeeeehhhhhhhhhhhhhhh...........eeee.....hhhhhhhhhhhhhhh...ee.......hhhhhhhhhhhhh..eeee.hhhhhhhheeeeee.....eeeee..hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4g84 A  55 VLKTPKGTRDYSPRQMAVREKVFDVIIRCFKRHGAEVIDTPVFELKETLMGKYGLIYDLKDQGGELLSLRYDLTVPFARYLAMNKLTNIKRYHIAKVYRRDNRYREFYQCDFDIAGNFDPMIPDAECLKIMCEILSSLQIGDFLVKVNDRRILDGMFAICGVSDSKFRTICSSVDKLDKVSWEEVKNEMVGEKGLAPEVADRIGDYVQQHGGVSLVEQLLQDPKLSQNKQALEGLGDLKLLFEYLTLFGIDDKISFDLSLARGLDYYTGVIYEAVLLQTPLGVGSVAAGGRYDGLVGMFDPKGRKVPCVGLSIGVERIFSIVEQRLEALEEKIRTTETQVLVASAQKKLLEERLKLVSELWDAGIKAELLYKKNPKLLNQLQYCEEAGIPLVAIIGEQELKDGVIKLRSVTSREEVDVRREDLVEEIKRRTGQ 504
                                    64        74        84        94       104   ||  118       128       138       148       158 ||    174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501   
                                                                               108|                                            160|                                                                                                                                                                             343|                                                                                                                                                         
                                                                                113                                             167                                                                                                                                                                              351                                                                                                                                                         


Chain B from PDB  Type:PROTEIN  Length:438
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhh..ee.....eeehhhhh..............eee...hhhhhhhhhhhh....eeeeeeeeee.......eeeeeeeeee.....hhhhhhhhhhhhhhhhhh....eeeeeeehhhhhhhhhhh..hhhhhhhhhhhhhhhhh.hhhhhhhhhhh....hhhhhhhhhhhhh.eehhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh.hhh.eeee............eeeeeee...eeeeeee..hhhhhhh.......eeeeeehhhhhhhhhhhhhhhh..........eeee.....hhhhhhhhhhhhhhh...ee.......hhhhhhhhhhhhh..eeee.hhhhhhh.eeeeee.....eeeee..hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4g84 B  43 GPGSEFELRRQFVLKTPKGTRDYSPRQMAVREKVFDVIIRCFKRHGAEVIDTPVFELKETLMSKLIYDLKDQGGELLSLRYDLTVPFARYLAMNKLTNIKRYHIAKVYRRDNRYREFYQCDFDIAGNFDPMIPDAECLKIMCEILSSLQIGDFLVKVNDRRILDGMFAICGVSDSKFRTICSSVDKLDKVSWEEVKNEMVGEKGLAPEVADRIGDYVQQHGGVSLVEQLLQDPKLSQNKQALEGLGDLKLLFEYLTLFGIDDKISFDLSLARGLDYYTGVIYEAVLLQGSVAAGGRYDGLVGMFDPKGRKVPCVGLSIGVERIFSIVEQRLEALEEKIRTTETQVLVASAQKKLLEERLKLVSELWDAGIKAELLYKKNPKLLNQLQYCEEAGIPLVAIIGEQELKDGVIKLRSVTSREEVDVRREDLVEEIKRRTGQ 504
                                    52        62        72        82        92       102 ||    118       128       138       148       158 ||    174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496        
                                                                                       104|                                              160|                                                                                                                                                                            342|                                                                                                                                                     
                                                                                        111                                               167                                                                                                                                                                             355
   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 4G84)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4G84)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4G84)

(-) Gene Ontology  (12, 12)

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 ]
    IMD  [ 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 4g84)
 

(-) 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
  4g84
    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
  SYHC_HUMAN | P12081
    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)
  6.1.1.21
    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
  SYHC_HUMAN | P12081
    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
        SYHC_HUMAN | P12081: 1x59 2lw7 4g85 4phc 4x5o

(-) Related Entries Specified in the PDB File

4g85 FULL LENGTH PROTEIN