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 GH3.12 IN COMPLEX WITH AMPCPP
 
Authors :  C. Zubieta, M. Nanao, J. Jez
Date :  28 Apr 12  (Deposition) - 13 Jun 12  (Release) - 25 Jul 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Firefly Luciferase Family, Adenylation, Amino Acid Conjugation, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. S. Westfall, C. Zubieta, J. Herrmann, U. Kapp, M. H. Nanao, J. M. Jez
Structural Basis For Prereceptor Modulation Of Plant Hormones By Gh3 Proteins.
Science V. 336 1708 2012
PubMed-ID: 22628555  |  Reference-DOI: 10.1126/SCIENCE.1221863

(-) Compounds

Molecule 1 - 4-SUBSTITUTED BENZOATES-GLUTAMATE LIGASE GH3.12
    Chains: A, B
    EC Number: 6.3.2.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: GH3.12, GDG1, PBS3, WIN3, AT5G13320, T22N19.5, T31B5.140
    Organism Common: MOUSE-EAR CRESS,THALE-CRESS
    Organism Scientific: ARABIDOPSIS THALIANA
    Organism Taxid: 3702
    Synonym: AUXIN-RESPONSIVE GH3-LIKE PROTEIN 12, ATGH3-12, PROTEIN GH3- LIKE DEFENSE GENE 1, PROTEIN GRETCHEN HAGEN 3.12, PROTEIN HOPW1-1- INTERACTING 3, PROTEIN AVRPPHB SUSCEPTIBLE 3

 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  (2, 3)

Asymmetric Unit (2, 3)
No.NameCountTypeFull Name
1APC2Ligand/IonDIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER
2MN1Ligand/IonMANGANESE (II) ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1APC1Ligand/IonDIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER
2MN-1Ligand/IonMANGANESE (II) ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1APC1Ligand/IonDIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER
2MN-1Ligand/IonMANGANESE (II) ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL A:299 , TYR A:325 , GLY A:326 , SER A:327 , TYR A:347 , ASP A:398 , PHE A:414 , LYS A:550 , MN A:602BINDING SITE FOR RESIDUE APC A 601
2AC2SOFTWAREAPC A:601BINDING SITE FOR RESIDUE MN A 602
3AC3SOFTWARESER A:80 , TYR B:325 , GLY B:326 , SER B:328 , LYS B:550BINDING SITE FOR RESIDUE APC B 601

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (9, 9)

Asymmetric Unit
No.Residues
1Thr A:19 -Ser A:20
2Pro A:107 -Trp A:108
3Phe A:464 -Pro A:465
4Thr A:546 -Gly A:547
5Ser A:557 -Gly A:558
6Thr B:19 -Ser B:20
7Gly B:100 -Gly B:101
8Phe B:464 -Pro B:465
9Ser B:557 -Gly B:558

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4EWV)

(-) 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:478
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhh....hhhhhhhhhhhhh..hhhhhh...hhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhh..................hhhhhhhhhhhh...........hhhhhh..hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhh..hhhhhhhhhhhhh......hhhhhh.....ee...hhhhhhhhhhhhhhh....ee..eee....eeeee...........eee............ee.........eeeeeeee....eeeeeeee...ee......eehhhhhhhhhhhhhhhhhh..eeeeeeeeee......eeeeeeeee......hhhhhhhhhhhhhh..hhhhhhhhh........eeeee..hhhhhhhhhhhhh.................hhhhhhhheeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ewv A   8 NETFEKQLKDLTSNVKSIQDNLLEEIITPDKELFKKNVSYEDIKPYLDRVVNGESQKMMPWNNKYLDNLTFIYDLRMQVITKHVKGVEMMFLFTKQEPARVATSSYFKSDYFKNRPSNWYYSYTSPDEVILCPNNTESLYCHLLCGLVQRGSIFASVMVRAIEVLKNSWEELCSNIRSGHLSNWVTDLGCQNSVSLVLGGPRPELADTIEEICNQNSWKGIVKRLWPNTKYIETVVTGSMGQYVPMLNYYCNDLPLVSTTYGSSETTFGINLDPLCKPEDVSYTFMPNMSYFEFIGCTYAGLYRMRVGDIVLVTGFYNNAPQFKFVRRENVVLSIDSDKTNEEDLFKAVSQAKLVLESSGLDLKDFTSYADTSTFPGHYVVYLEVDTKQFELDEEALSTCCLVMEESLDNVYKRCRFKDGSIGPLEIRVVRQGTFDSLMDFFISQGASTGQYKTPRCIKSGKALQVLETCVVAKFFSI 575
                                    17        27        52       |65        75    || 107       117       127       141      |158       168       178       188       198       208|      224       234       244       254       264       274       284       294       304       314       324       334       344       354    || 389       399       409       419       429       439       449       459       469       487       497       507       517       527       537       547       557       567        
                                                       36|      60|              80|                             135|     148|                                                 208|                                                                                                                                             359|  ||                                                                                     477|                                                                                         
                                                        52       64              103                              140      156                                                  215                                                                                                                                              378  ||                                                                                      486                                                                                         
                                                                                                                                                                                                                                                                                                                                    381|                                                                                                                                                                                  
                                                                                                                                                                                                                                                                                                                                     389                                                                                                                                                                                  


Chain B from PDB  Type:PROTEIN  Length:492
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhh...hhhhhhhhhhhhhhhh...hhhhhhhh..ee...hhhhhhhhh.................hhhhhhhhhhhhhhhhhhhh.....ee...........hhhhhhhhhhhh...........hhhhhh..hhhhhhhhhhhhhhhh......eeeeehhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhh..hhhhhhhhhhhhh.................eeee.hhhhhhhhhhhhhhh....ee..eee....eeeee...........ee..........ee........ee..eeeeeeee....eeeeeeee...ee......eehhhhhhhhhhhhhhhhh...eeeeeeeeee......eeeeeeeee......hhhhhhhhhhhh....hhhhhhh..........eeeee..hhhhhhhhhhhhh..............hhhhhhhheeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4ewv B   8 NETFEKQLKDLTSNVKSIQDNLLEEIITPNTKTDKELFKKNVPIVSYEDIKPYLDRVVNGESSGGAQKMMPWNNKYLDNLTFIYDLRMQVITKHVKGVEGMMFLFTKQEARVATSSYFKSDYFKNRPSNWYYSYTSPDEVILCPNNTESLYCHLLCGLVQRDEVVRTGSIFASVMVRAIEVLKNSWEELCSNIRSGHLSNWVTDLGCQNSVSLVLGGPRPELADTIEEICNQNSWKGIVKRLWPNTKYIETVVTGSMGQYVPMLNYYCNDLPLVSTTYGSSETTFGINLDPLCKPEDVSYTFSYFEFKLGCTYEPVAGLYRMRVGDIVLVTGFYNNAPQFKFVRRENVVLSIDSDKTNEEDLFKAVSQAKLVLESSGLDLKDFTSYADTSTFPGHYVVYLEVDTKQFELDEEALSTCCLVMEESLDNVYKRCRFKDGSIGPLEIRVVRQGTFDSLMDFFISQGASTKTPRCIKSGKALQVLETCVVAKFFSI 575
                                    17        27        37  ||    58        68        78 ||    106       116       126       139       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347 ||   |378     ||392       402       412       422       432       442       452       462       472    || 490       500       510       520       530       540     ||553       563       573  
                                                           40|                          80|                                 135|      148|                                                                                                                                                                                             349| 358|     384|                                                                                     477|                                                         546|                         
                                                            52                           99                                  139       157                                                                                                                                                                                              354  376      389                                                                                      486                                                          550
   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 4EWV)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (6, 6)

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
    APC  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Gly B:100 - Gly B:101   [ RasMol ]  
    Phe A:464 - Pro A:465   [ RasMol ]  
    Phe B:464 - Pro B:465   [ RasMol ]  
    Pro A:107 - Trp A:108   [ RasMol ]  
    Ser A:557 - Gly A:558   [ RasMol ]  
    Ser B:557 - Gly B:558   [ RasMol ]  
    Thr A:19 - Ser A:20   [ RasMol ]  
    Thr A:546 - Gly A:547   [ RasMol ]  
    Thr B:19 - Ser B:20   [ RasMol ]  
 
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
  4ewv
    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
  GH312_ARATH | Q9LYU4
    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)
  6.3.2.-
    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
  GH312_ARATH | Q9LYU4
    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
        GH312_ARATH | Q9LYU4: 4epm 4eq4 4eql 4l39

(-) Related Entries Specified in the PDB File

4epl 4epm 4eq4 4eql