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(-) Description

Title :  STRUCTURE OF ARABIDOPSIS DIRIGENT PROTEIN ATDIR6
 
Authors :  R. Gasper, P. Kolesinski, B. Terlecka, I. Effenberger, A. Schaller, E.
Date :  14 Jun 16  (Deposition) - 09 Nov 16  (Release) - 07 Dec 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.40
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (3x)
Biol. Unit 2:  B  (3x)
Keywords :  All Beta, Protein Binding, Plant Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  R. Gasper, I. Effenberger, P. Kolesinski, B. Terlecka, E. Hofmann, A. Schaller
Dirigent Protein Mode Of Action Revealed By The Crystal Structure Of Atdir6.
Plant Physiol. V. 172 2165 2016
PubMed-ID: 27756822  |  Reference-DOI: 10.1104/PP.16.01281

(-) Compounds

Molecule 1 - DIRIGENT PROTEIN 6
    ChainsA, B
    EngineeredYES
    Expression SystemARABIDOPSIS THALIANA
    Expression System CommonTHALE CRESS
    Expression System PlasmidPART27
    Expression System Taxid3702
    Expression System Vector TypePLASMID
    GeneDIR6, AT4G23690, F9D16.160
    Organism CommonTHALE CRESS
    Organism ScientificARABIDOPSIS THALIANA
    Organism Taxid3702
    SynonymATDIR6

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (3x)A 
Biological Unit 2 (3x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (7, 36)

Asymmetric Unit (7, 36)
No.NameCountTypeFull Name
1BMA3Ligand/IonBETA-D-MANNOSE
2EDO8Ligand/Ion1,2-ETHANEDIOL
3FUC3Ligand/IonALPHA-L-FUCOSE
4GLY5Mod. Amino AcidGLYCINE
5MAN6Ligand/IonALPHA-D-MANNOSE
6NAG8Ligand/IonN-ACETYL-D-GLUCOSAMINE
7XYP3Ligand/IonBETA-D-XYLOPYRANOSE
Biological Unit 1 (7, 48)
No.NameCountTypeFull Name
1BMA3Ligand/IonBETA-D-MANNOSE
2EDO15Ligand/Ion1,2-ETHANEDIOL
3FUC3Ligand/IonALPHA-L-FUCOSE
4GLY6Mod. Amino AcidGLYCINE
5MAN6Ligand/IonALPHA-D-MANNOSE
6NAG12Ligand/IonN-ACETYL-D-GLUCOSAMINE
7XYP3Ligand/IonBETA-D-XYLOPYRANOSE
Biological Unit 2 (7, 60)
No.NameCountTypeFull Name
1BMA6Ligand/IonBETA-D-MANNOSE
2EDO9Ligand/Ion1,2-ETHANEDIOL
3FUC6Ligand/IonALPHA-L-FUCOSE
4GLY9Mod. Amino AcidGLYCINE
5MAN12Ligand/IonALPHA-D-MANNOSE
6NAG12Ligand/IonN-ACETYL-D-GLUCOSAMINE
7XYP6Ligand/IonBETA-D-XYLOPYRANOSE

(-) Sites  (20, 20)

Asymmetric Unit (20, 20)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREBMA A:203 , XYP A:205binding site for residue MAN A 206
02AC2SOFTWARENAG A:201 , NAG A:202binding site for residue FUC A 207
03AC3SOFTWAREVAL A:165 , THR A:166 , ASP A:167 , BMA B:203binding site for residue EDO A 210
04AC4SOFTWAREASP A:154 , PHE A:155 , PHE A:156 , ALA A:158 , CYS A:186 , TYR A:187 , LYS B:37binding site for residue EDO A 211
05AC5SOFTWAREVAL A:97 , ALA A:98 , ASN A:123 , HOH A:352 , HOH A:370binding site for residue EDO A 212
06AC6SOFTWAREALA A:64 , ILE A:65 , VAL A:66 , SER B:67 , EDO B:217binding site for residue EDO A 213
07AC7SOFTWAREASP A:111 , PHE A:112 , MET A:139 , MET A:140binding site for residue EDO A 214
08AC8SOFTWARETYR A:106 , SER A:114 , PHE A:116 , ASP A:137 , MET A:139 , PHE A:175binding site for residue GLY A 215
09AC9SOFTWAREGLU A:126 , HIS A:127 , HOH A:319binding site for residue GLY A 216
10AD1SOFTWAREBMA B:203 , XYP B:205binding site for residue MAN B 207
11AD2SOFTWAREVAL B:165 , ASP B:167binding site for residue EDO B 215
12AD3SOFTWAREVAL B:97 , ALA B:98 , PHE B:122 , ASN B:123 , HOH B:334 , HOH B:376binding site for residue EDO B 216
13AD4SOFTWARESER A:67 , EDO A:213 , ALA B:64 , ILE B:65 , VAL B:66binding site for residue EDO B 217
14AD5SOFTWARETYR B:106 , SER B:114 , PHE B:116 , ASP B:137 , MET B:139 , PHE B:169 , PHE B:175binding site for residue GLY B 218
15AD6SOFTWAREPHE B:45 , HIS B:127 , HOH B:303 , HOH B:332binding site for residue GLY B 219
16AD7SOFTWAREMET B:108 , PHE B:112 , ASN B:113 , LEU B:138 , MET B:139 , MET B:140 , GLU B:141binding site for residue GLY B 220
17AD8SOFTWAREASN A:59 , TYR A:92 , GLN A:170 , TYR A:174 , MAN A:206 , FUC A:207 , HOH A:303 , HOH A:305 , HOH A:307 , HOH A:315 , HOH A:324 , HOH A:330 , HOH A:340 , HOH A:350 , HOH A:353 , ASP B:89 , ASN B:91 , SER B:94binding site for Poly-Saccharide residues NAG A 201 through XYP A 205 bound to ASN A 59
18AD9SOFTWAREASN A:123 , GLU A:141 , HOH A:391binding site for Poly-Saccharide residues NAG A 208 through NAG A 209 bound to ASN A 123
19AE1SOFTWAREPRO A:142 , VAL A:165 , THR A:166 , ASP A:167 , EDO A:210 , ILE B:50 , ASN B:59 , TYR B:92 , GLN B:170 , TYR B:174 , MAN B:207 , HOH B:302 , HOH B:311 , HOH B:331 , HOH B:336 , HOH B:354 , HOH B:361 , HOH B:374 , HOH B:375binding site for Poly-Saccharide residues NAG B 201 through FUC B 206 bound to ASN B 59
20AE2SOFTWARELYS A:41 , THR A:125 , GLU A:126 , HIS A:127 , LYS A:128 , ASP A:154 , ASN B:123 , GLU B:141binding site for Poly-Saccharide residues NAG B 208 through FUC B 214 bound to ASN B 123

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:40 -A:186
2B:40 -B:186

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5LAL)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5LAL)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5LAL)

(-) Exons   (0, 0)

(no "Exon" information available for 5LAL)

(-) 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:153
                                                                                                                                                                                         
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeeeeee...........eee..............eeeeeeeee..........eeeeeeeee.......eeeeeeeeee....eeeeeeeeee......eeeeeeeeee.....eeeeeeeeeeee...eeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5lal A  35 DQKKPCKHFSFYFHDILYDGDNVANATSAAIVSPPGLGNFKFGKFVIFDGPITMDKNYLSKPVARAQGFYFYDMKMDFNSWFSYTLVFNSTEHKGTLNIMGADLMMEPTRDLSVVGGTGDFFMARGIATFVTDLFQGAKYFRVKMDIKLYECY 187
                                    44        54        64        74        84        94       104       114       124       134       144       154       164       174       184   

Chain B from PDB  Type:PROTEIN  Length:155
                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee.....eeeeeeeeee...........eee..............eeeeeeeee..........eeeeeeeee.......eeeeeeeeee....eeeeeeeeee......eeeeeeeeee.....eeeeeeeeeeee...eeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5lal B  33 TIDQKKPCKHFSFYFHDILYDGDNVANATSAAIVSPPGLGNFKFGKFVIFDGPITMDKNYLSKPVARAQGFYFYDMKMDFNSWFSYTLVFNSTEHKGTLNIMGADLMMEPTRDLSVVGGTGDFFMARGIATFVTDLFQGAKYFRVKMDIKLYECY 187
                                    42        52        62        72        82        92       102       112       122       132       142       152       162       172       182     

   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 5LAL)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5LAL)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5LAL)

(-) Gene Ontology  (7, 7)

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