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 HUMAN ALARS CATALYTIC DOMAIN WITH R329H MUTATION
 
Authors :  H. Zhou, W. He, X. L. Yang
Date :  24 Dec 14  (Deposition) - 30 Dec 15  (Release) - 30 Dec 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.38
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Trna Synthetase, Ligase, Cmt (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  X. L. Yang
Crystal Structure Of Human Alars Catalytic Domain With R329 Mutation
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - ALANINE--TRNA LIGASE, CYTOPLASMIC
    Chains: A, B
    EC Number: 6.1.1.7
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: CATALYTIC DOMAIN
    Gene: AARS
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: C-TER FRAGMENT GOT DEGRADED DURING CRYSTALLIZATION
    Synonym: ALANYL-TRNA SYNTHETASE,ALARS,RENAL CARCINOMA ANTIGEN NY-REN- 42

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 12)

Asymmetric Unit (4, 12)
No.NameCountTypeFull Name
1A5A2Ligand/Ion'5'-O-(N-(L-ALANYL)-SULFAMOYL)ADENOSINE
2GOL4Ligand/IonGLYCEROL
3MG2Ligand/IonMAGNESIUM ION
4SO44Ligand/IonSULFATE ION
Biological Unit 1 (3, 5)
No.NameCountTypeFull Name
1A5A1Ligand/Ion'5'-O-(N-(L-ALANYL)-SULFAMOYL)ADENOSINE
2GOL2Ligand/IonGLYCEROL
3MG-1Ligand/IonMAGNESIUM ION
4SO42Ligand/IonSULFATE ION
Biological Unit 2 (3, 5)
No.NameCountTypeFull Name
1A5A1Ligand/Ion'5'-O-(N-(L-ALANYL)-SULFAMOYL)ADENOSINE
2GOL2Ligand/IonGLYCEROL
3MG-1Ligand/IonMAGNESIUM ION
4SO42Ligand/IonSULFATE ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREALA A:44 , ARG A:77 , TYR A:93 , HIS A:94 , HIS A:95 , PHE A:98 , MET A:100 , TRP A:176 , GLU A:213 , ILE A:214 , ASN A:216 , VAL A:218 , ASP A:239 , THR A:240 , GLY A:241 , GLY A:243 , ARG A:246 , HOH A:689 , HOH A:695binding site for residue A5A A 501
02AC2SOFTWAREHIS A:27 , SER A:28 , SER A:29 , ALA A:30 , LYS A:74 , GLU A:363 , HOH A:721 , HOH A:736 , HOH A:831 , HOH A:867 , GLU B:268binding site for residue GOL A 502
03AC3SOFTWAREGLN A:12 , ILE A:15 , LYS A:19 , HOH A:826binding site for residue GOL A 503
04AC4SOFTWARETYR A:109 , PHE A:110 , GLU A:112 , LEU A:113 , HOH A:763 , HOH A:845binding site for residue SO4 A 504
05AC5SOFTWAREASP A:86 , ARG A:330 , ARG A:333 , TYR A:334binding site for residue SO4 A 505
06AC6SOFTWAREGLU A:189 , GLU A:213 , HOH A:784 , HOH A:820 , HOH A:863 , HOH A:1016binding site for residue MG A 506
07AC7SOFTWAREALA B:44 , ARG B:77 , TYR B:93 , HIS B:94 , HIS B:95 , PHE B:98 , MET B:100 , TRP B:176 , GLU B:213 , ILE B:214 , ASN B:216 , VAL B:218 , ASP B:239 , THR B:240 , GLY B:241 , GLY B:243 , ARG B:246 , HOH B:651 , HOH B:653 , HOH B:747 , HOH B:893binding site for residue A5A B 501
08AC8SOFTWAREGLN B:12 , ILE B:15 , LYS B:19 , HOH B:605binding site for residue GOL B 502
09AC9SOFTWAREGLU A:268 , HIS B:27 , SER B:28 , SER B:29 , ALA B:30 , LYS B:74 , GLU B:363 , HOH B:601 , HOH B:608 , HOH B:610 , HOH B:614binding site for residue GOL B 503
10AD1SOFTWAREASP B:86 , ARG B:330 , ARG B:333 , TYR B:334binding site for residue SO4 B 504
11AD2SOFTWARETYR B:109 , PHE B:110 , GLU B:112 , LEU B:113 , HOH B:713 , HOH B:968binding site for residue SO4 B 505
12AD3SOFTWAREGLU B:189 , GLU B:213 , HOH B:714 , HOH B:771 , HOH B:976 , HOH B:977binding site for residue MG B 506

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4XEO)

(-) 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:384
                                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhh..ee..................hhhhhhhhhhh......hhhhhh.eeeeeeeee...................eeeeeeeee....hhhhhhhhhhhhhhh....hhh.eeeeee..........hhhhhhhhhhh..hhh.eeeehhhhhee.....eeeeeeeeeeee......hhhhh......eeeeeeeeeeeeee.....eeeeeeeeeeeeeehhhhhhhhh...hhhhh..hhhhhhhhhhhhh.......hhhhh..hhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4xeo A   4 TLTASEIRQRFIDFFKRNEHTYVHSSATIPLDDPTLLFANAGMNQFKPIFLNTIDPSHPMAKLSRAANTQKCIRAGGKHNLDDVGKDVYHHTFFEMLGSWSFGDYFKELACKMALELLTQEFGIPIERLYVTYFGGDEAAGLEADLECKQIWQNLGLDDTKILPGNMKDNFWEMGDTGPCGPCSEIHYDRIGGRDAAHLVNQDDPNVLEIWNLVFIQYNREADGILKPLPKKSIDTGMGLERLVSVLQNKMSNYDTDLFVPYFEAIQKGTGARPYTGKVGAEDADGIDMAYRVLADHARTITVALADGGRPDNTGRGYVLRRILHRAVRYAHEKLNASRGFFATLVDVVVQSLGDAFPELKKDPDMVKDIINEEEVQFLKTLSR 388
                                    13        23        33        43        53        63        73        83|       94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384    
                                                                                                          83|                                                                                                                                                                                                                                                                                                               
                                                                                                           85                                                                                                                                                                                                                                                                                                               


Chain B from PDB  Type:PROTEIN  Length:378
                                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhh..ee..................hhhhhhhhhhh......hhhhhh.eeeeeeeee..hhhhh........eeeeeeeee....hhhhhhhhhhhhhhh....hhh.eeeeee..........hhhhhhhhhhh..hhh.eeeehhhhhee.....eeeeeeeeeeee......hhhhh......eeeeeeeeeeeeee.....eeeeeeeeeeeeeehhhhhhhhh...hhhhh..hhhhhhhhhhhhh.......hhhhh..hhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4xeo B   3 STLTASEIRQRFIDFFKRNEHTYVHSSATIPLDDPTLLFANAGMNQFKPIFLNTIDPSHPMAKLSRAANTQKCIRADLDDVGKDVYHHTFFEMLGSWSFGDYFKELACKMALELLTQEFGIPIERLYVTYFGGDEAAGLEADLECKQIWQNLGLDDTKILPGNMKDNFWEMGDTGPCGPCSEIHYDRIGGRDAAHLVNQDDPNVLEIWNLVFIQYNREADGILKPLPKKSIDTGMGLERLVSVLQNKMSNYDTDLFVPYFEAIQKGTGARPYTGKVGAEDADGIDMAYRVLADHARTITVALADGGRPDNTGRGYVLRRILHRAVRYAHEKLNASRGFFATLVDVVVQSLGDAFPELKKDPDMVKDIINEEEVQFLKT 385
                                    12        22        32        42        52        62        72     || 87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377        
                                                                                                      78|                                                                                                                                                                                                                                                                                                             
                                                                                                       84
   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 4XEO)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (35, 35)

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
    A5A  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MG  [ 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 ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    AD1  [ RasMol ]  +environment [ RasMol ]
    AD2  [ RasMol ]  +environment [ RasMol ]
    AD3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4xeo)
 
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
  4xeo
    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
  SYAC_HUMAN | P49588
    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)
  6.1.1.7
    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
  SYAC_HUMAN | P49588
    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
        SYAC_HUMAN | P49588: 4xem 5knn 5t5s 5t76

(-) Related Entries Specified in the PDB File

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