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 ENGINEERED BRADYRHIZOBIUM JAPONICUM GLYCINE:[CARRIER PROTEIN] LIGASE COMPLEXED WITH CARRIER PROTEIN FROM AGROBACTERIUM TUMEFACIENS AND AN ANALOGUE OF GLYCYL ADENYLATE
 
Authors :  M. Luic, I. Weygand-Durasevic, N. Ivic, M. Mocibob
Date :  13 Sep 12  (Deposition) - 06 Mar 13  (Release) - 19 Jun 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.15
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Ligase, Atp Binding, Glycine Binding, Carrier Protein, Aminoacyl-Trna Synthetase, Seryl-Trna Synthetase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Mocibob, N. Ivic, M. Luic, I. Weygand-Durasevic
Adaptation Of Aminoacyl-Trna Synthetase Catalytic Core To Carrier Protein Aminoacylation.
Structure V. 21 614 2013
PubMed-ID: 23541895  |  Reference-DOI: 10.1016/J.STR.2013.02.017
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - AMINO ACID--[ACYL-CARRIER-PROTEIN] LIGASE 1
    Chains: A
    EC Number: 6.2.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: BLL0957
    Organism Scientific: BRADYRHIZOBIUM JAPONICUM
    Organism Taxid: 224911
    Strain: USDA 110
    Synonym: AMINOACYL-[ACYL-CARRIER-PROTEIN] SYNTHETASE 1
 
Molecule 2 - AMINO ACID--[ACYL-CARRIER-PROTEIN] LIGASE 1
    Chains: B
    EC Number: 6.2.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: BLL0957
    Organism Scientific: BRADYRHIZOBIUM JAPONICUM
    Organism Taxid: 224911
    Strain: USDA 110
    Synonym: AMINOACYL-[ACYL-CARRIER-PROTEIN] SYNTHETASE 1
 
Molecule 3 - AMINOACYL CARRIER PROTEIN
    Chains: C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: AGR_C_4658, ATU2571
    Organism Scientific: AGROBACTERIUM TUMEFACIENS
    Organism Taxid: 176299
    Strain: C58

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 9)

Asymmetric/Biological Unit (5, 9)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2CSO2Mod. Amino AcidS-HYDROXYCYSTEINE
3G5A2Ligand/Ion5'-O-(GLYCYLSULFAMOYL)ADENOSINE
4PNS2Ligand/Ion4'-PHOSPHOPANTETHEINE
5ZN1Ligand/IonZINC ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:129 , CSO A:131 , ARG A:159 , LEU A:169 , PHE A:172 , MET A:174 , GLU A:176 , LYS A:235 , ALA A:250 , CYS A:251 , SER A:253 , ASN A:255 , CSO A:279 , ALA A:281 , GLY A:283 , ARG A:286 , CL A:402 , HOH A:638 , PNS D:101BINDING SITE FOR RESIDUE G5A A 401
2AC2SOFTWAREGLY A:283 , MET A:284 , ASP A:285 , ARG A:286 , G5A A:401BINDING SITE FOR RESIDUE CL A 402
3AC3SOFTWARECYS B:131 , GLU B:176 , CYS B:279 , G5A B:402BINDING SITE FOR RESIDUE ZN B 401
4AC4SOFTWAREALA B:129 , CYS B:131 , ARG B:159 , GLU B:161 , LEU B:169 , PHE B:172 , MET B:174 , GLU B:176 , LYS B:235 , ALA B:250 , CYS B:251 , MET B:252 , SER B:253 , ASN B:255 , ALA B:281 , GLY B:283 , ARG B:286 , ZN B:401 , CL B:403 , HOH B:575 , HOH B:626 , PNS C:101BINDING SITE FOR RESIDUE G5A B 402
5AC5SOFTWAREGLY B:283 , MET B:284 , ASP B:285 , ARG B:286 , G5A B:402BINDING SITE FOR RESIDUE CL B 403
6AC6SOFTWARETYR B:132 , ASP B:215 , ASN B:228 , GLN B:232 , LEU B:234 , HIS B:257 , HIS B:260 , G5A B:402 , HOH B:613 , HOH B:677 , HOH B:682 , SER C:35BINDING SITE FOR RESIDUE PNS C 101
7AC7SOFTWARECSO A:131 , TYR A:132 , ASP A:215 , ASN A:228 , GLN A:232 , HIS A:257 , HIS A:260 , G5A A:401 , HOH A:592 , SER D:35 , PHE D:36BINDING SITE FOR RESIDUE PNS D 101

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4H2X)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4H2X)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4H2X)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4H2X)

(-) Exons   (0, 0)

(no "Exon" information available for 4H2X)

(-) 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:295
                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhheeeeee..eeeehhhhhhhhhhhhhhhhhh....eeeee...eeehhhhhhhhhhhhhhhhheeeee...hhhhhhhhhhhhhhh.hhhhhheeeeeee......hhhhhhhh........eeeeeeeeee............eeeeeeeeeeehhhhhhhhhhhhhhhhhhhhhhh....eeee.....hhhhhhhhhhhhhhh..eeeeee........eeeeeeee..hhhhhhh..........eeeeeeeehhhhhhhhhhhhh.hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4h2x A  18 DPLDHLADKLFHSMGSDGVYARTALYESIVERLAALITSHREAGTEALRFPPVMSRAQLEKSGYLKSFPNLLGCVCGLHGTEREINAAVSRFDAGGDWTTSLSPADLVLSPAAcYPVYPIAASRGPLPKGGLRFDVAADCFRREPSKHLDRLQSFRMREYVCIGTPDDVSDFRERWMVRAQAIARDLGLTFRVDYASDPFFGRAGKMLANNQRDQQLKFELLIPLRSEEQPTACMSFNYHREHFGTTWGIQDANGEPAHTGcVAFGMDRLAVAMFHTHGTDLSAWPAKVRDILGL 312
                                    27        37        47        57        67        77        87        97       107       117       127   |   137       147       157       167       177       187       197       207       217       227       237       247       257       267       277 |     287       297       307     
                                                                                                                                           131-CSO                                                                                                                                             279-CSO                             


Chain B from PDB  Type:PROTEIN  Length:296
                                                                                                                                                                                                                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhheee......eeeehhhhhhhhhhhhhhhhh....eeeee...eeehhhhhhhhhhhhhhhhh.eeee...hhhhhhhhhhhhhh..hhhhhheeeeeee......hhhhhhhh........eeeeeeeeee............eeeeeeeeeeehhhhhhhhhhhhhhhhhhhhhhh....eeee.....hhhhhhhhhhhhhhh..eeeeee........eeeeeeee..hhhhhhh..........eeeeeeeehhhhhhhhhhhhh.hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4h2x B  17 ADPLDHLADKLFHSMGSDGVYARTALYESIVERLAALITSHREAGTEALRFPPVMSRAQLEKSGYLKSFPNLLGCVCGLHGTEREINAAVSRFDAGGDWTTSLSPADLVLSPAACYPVYPIAASRGPLPKGGLRFDVAADCFRREPSKHLDRLQSFRMREYVCIGTPDDVSDFRERWMVRAQAIARDLGLTFRVDYASDPFFGRAGKMLANNQRDQQLKFELLIPLRSEEQPTACMSFNYHREHFGTTWGIQDANGEPAHTGCVAFGMDRLAVAMFHTHGTDLSAWPAKVRDILGL 312
                                    26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306      


Chain C from PDB  Type:PROTEIN  Length:77
                                                                                                             
               SCOP domains d4h2xc_ C: automated matches                                                  SCOP domains
               CATH domains ----------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh.....hhhhh....hhhhhh.hhhhhhhhhhhhhhhh....hhhhh.hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------- Transcript
                 4h2x C   0 HMNATIREILAKFGQLPTPVDTIADEADLYAAGLSSFASVQLMLGIEEAFDIEFPDNLLNRKSFASIKAIEDTVKLI  76
                                     9        19        29        39        49        59        69       


Chain D from PDB  Type:PROTEIN  Length:75
                                                                                                           
               SCOP domains d4h2xd_ D: automated matches                                                SCOP domains
               CATH domains --------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhh..............hhhhhh.hhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------- Transcript
                 4h2x D   1 MNATIREILAKFGQLPTPVDTIADEADLYAAGLSSFASVQLMLGIEEAFDIEFPDNLLNRKSFASIKAIEDTVKL  75
                                    10        20        30        40        50        60        70
   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, 2)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4H2X)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4H2X)

(-) Gene Ontology  (7, 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 ]
    CSO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    G5A  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PNS  [ 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 ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4h2x)
 

(-) 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
  4h2x
    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
  AACL1_BRADU | Q89VT8
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  AACL_AGRFC | Q7CWR3
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  AACP_AGRFC | A9CHM9
    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)
  6.2.1.-
    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
  AACL1_BRADU | Q89VT8
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  AACL_AGRFC | Q7CWR3
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  AACP_AGRFC | A9CHM9
    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
        AACL1_BRADU | Q89VT8: 3mey 3mf1 3mf2 3pzc 4h2s 4h2t 4h2u 4h2v 4h2w 4h2y
        AACL_AGRFC | Q7CWR3: 4h2w 4h2y
        AACP_AGRFC | A9CHM9: 2jq4 4h2w 4h2y

(-) Related Entries Specified in the PDB File

3mf2 THE SAME ENZYME BUT NOT COMPLEXED WITH COGNATE CARRIER PROTEIN
4h2s
4h2t
4h2u
4h2v
4h2w
4h2y