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(-) Description

Title :  DEBP
 
Authors :  Y. L. Hu, C. -P. Fan, G. S. Fu, D. Y. Zhu, Q. Jin, D. -C. Wang
Date :  20 Nov 07  (Deposition) - 08 Jul 08  (Release) - 24 Mar 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Transport Protein, Periplasmic Binding Protein, Crystal Structure, Ligand Binding, Ultrahigh Resolution, Structural Basis Of Structural Basis Of Specificity, Shigella Flexneri (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. L. Hu, C. -P. Fan, G. S. Fu, D. Y. Zhu, Q. Jin, D. -C. Wang
Crystal Structure Of A Glutamate/Aspartate Binding Protein Complexed With A Glutamate Molecule: Structural Basis Of Ligand Specificity At Atomic Resolution.
J. Mol. Biol. V. 382 99 2008
PubMed-ID: 18640128  |  Reference-DOI: 10.1016/J.JMB.2008.06.091

(-) Compounds

Molecule 1 - PERIPLASMIC BINDING TRANSPORT PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET22B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Fragment: RESIDUES 24-302
    Organism Scientific: SHIGELLA FLEXNERI
    Organism Taxid: 623
    Synonym: PERIPLASMIC GLUTAMATE-ASPARTATE BINDING PROTEIN

 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
1GLU2Mod. Amino AcidGLUTAMIC ACID
2TRS2Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:24 , SER A:72 , ARG A:75 , SER A:90 , THR A:91 , THR A:92 , ARG A:97 , THR A:139 , THR A:140 , HIS A:164 , MET A:181 , ASP A:182 , LEU A:185 , TYR A:211BINDING SITE FOR RESIDUE GLU A1280
2AC2SOFTWAREARG B:24 , SER B:72 , ARG B:75 , SER B:90 , THR B:91 , THR B:92 , ARG B:97 , THR B:139 , THR B:140 , HIS B:164 , MET B:181 , ASP B:182 , LEU B:185 , TYR B:211BINDING SITE FOR RESIDUE GLU B1280
3AC3SOFTWAREASP B:105 , ASP B:227 , ASN B:274 , ASP B:275 , HOH B:2300 , HOH B:2360BINDING SITE FOR RESIDUE TRS B1281
4AC4SOFTWAREASP A:105 , ASP A:227 , ASN A:274 , ASP A:275 , HOH A:2315 , HOH A:2370BINDING SITE FOR RESIDUE TRS A1281

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:88 -A:213
2B:88 -B:213

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Val A:28 -Pro A:29
2Pro A:252 -Pro A:253
3Val B:28 -Pro B:29
4Pro B:252 -Pro B:253

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2VHA)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2VHA)

(-) Exons   (0, 0)

(no "Exon" information available for 2VHA)

(-) 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:278
 aligned with A0A0H2VVF4_S | A0A0H2VVF4 from UniProtKB/TrEMBL  Length:302

    Alignment length:278
                                                                                                                                                                                                                                                                                                              302 
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295      | 
        A0A0H2VVF4_S     26 APAAGSTLDKIAKNGVIVVGHRESSVPFSYYDNQQKVVGYSQDYSNAIVEAVKKKLNKPDLQVKLIPITSQNRIPLLQNGTFDFECGSTTNNVERQKQAAFSDTIFVVGTRLLTKKGGDIKDFADLKGKAVVVTSGTTSEVLLNKLNEEQKMNMRIISAKDHGDSFRTLESGRAVAFMMDDALLAGERAKAKKPDNWDIVGKPQSQEAYGCMLRKDDPQFKKLMDDTIAQVQTSGEAEKWFDKWFKNPIPPKNLNMNFELSDEMKALFKEPNDKALN-    -
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhheeeeee..ee...eee.....eehhhhhhhhhhhhhhhhhh.....eeeeee....hhhhhhhh....ee......hhhhhh..eeeeeeeeeeeeeeee......hhhhhh..eeeee..hhhhhhhhhhhhhh....eeeee.hhhhhhhhhhh....eeeeehhhhhhhhh...hhh.eeee.....eeeeeeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2vha A    3 APAAGSTLDKIAKNGVIVVGHRESSVPFSYYDNQQKVVGYSQDYSNAIVEAVKKKLNKPDLQVKLIPITSQNRIPLLQNGTFDFECGSTTNNVERQKQAAFSDTIFVVGTRLLTKKGGDIKDFADLKGKAVVVTSGTTSEVLLNKLNEEQKMNMRIISAKDHGDSFRTLESGRAVAFMMDDALLAGERAKAKKPDNWDIVGKPQSQEAYGCMLRKDDPQFKKLMDDTIAQVQTSGEAEKWFDKWFKNPIPPKNLNMNFELSDEMKALFKEPNDKALNE 1280
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272      ||
                                                                                                                                                                                                                                                                                                              279|
                                                                                                                                                                                                                                                                                                              1280


Chain B from PDB  Type:PROTEIN  Length:278
 aligned with A0A0H2VVF4_S | A0A0H2VVF4 from UniProtKB/TrEMBL  Length:302

    Alignment length:278
                                                                                                                                                                                                                                                                                                              302 
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295      | 
        A0A0H2VVF4_S     26 APAAGSTLDKIAKNGVIVVGHRESSVPFSYYDNQQKVVGYSQDYSNAIVEAVKKKLNKPDLQVKLIPITSQNRIPLLQNGTFDFECGSTTNNVERQKQAAFSDTIFVVGTRLLTKKGGDIKDFADLKGKAVVVTSGTTSEVLLNKLNEEQKMNMRIISAKDHGDSFRTLESGRAVAFMMDDALLAGERAKAKKPDNWDIVGKPQSQEAYGCMLRKDDPQFKKLMDDTIAQVQTSGEAEKWFDKWFKNPIPPKNLNMNFELSDEMKALFKEPNDKALN-    -
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhheeeeee..ee...eee.....eehhhhhhhhhhhhhhhhhh.....eeeeee....hhhhhhhh....ee......hhhhhh..eeeeeeeeeeeeeeee......hhhhhh..eeeee..hhhhhhhhhhhhhh....eeeee.hhhhhhhhhhh....eeeeehhhhhhhhh...hhh.eeee.....eeeeeeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2vha B    3 APAAGSTLDKIAKNGVIVVGHRESSVPFSYYDNQQKVVGYSQDYSNAIVEAVKKKLNKPDLQVKLIPITSQNRIPLLQNGTFDFECGSTTNNVERQKQAAFSDTIFVVGTRLLTKKGGDIKDFADLKGKAVVVTSGTTSEVLLNKLNEEQKMNMRIISAKDHGDSFRTLESGRAVAFMMDDALLAGERAKAKKPDNWDIVGKPQSQEAYGCMLRKDDPQFKKLMDDTIAQVQTSGEAEKWFDKWFKNPIPPKNLNMNFELSDEMKALFKEPNDKALNE 1280
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272      ||
                                                                                                                                                                                                                                                                                                              279|
                                                                                                                                                                                                                                                                                                              1280
   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 2VHA)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2VHA)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2VHA)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 2VHA)

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  2vha
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  A0A0H2VVF4_S | A0A0H2VVF4
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 Related Entries

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UniProtKB/TrEMBL
        A0A0H2VVF4_S | A0A0H2VVF4: 2ia4

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