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(-) Description

Title :  CRYSTAL STRUCTURE OF ASPARTATE BETA-SEMIALDEHIDE DEHYDROGENASE FROM STREPTOCOCCUS PNEUMONIAE WITH 2',5'-ADENOSINE DIPHOSPHATE AND D-2-AMINOADIPATE
 
Authors :  A. G. Pavlovsky, R. E. Viola
Date :  08 Dec 10  (Deposition) - 04 Jan 12  (Release) - 04 Jan 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Dehydrogenase, Nadp Binding, Oxidoreductase-Oxidoreductase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. G. Pavlovsky, X. Liu, C. R. Faehnle, N. Potente, R. E. Viola
Structural Characterization Of Inhibitors With Selectivity Against Members Of A Homologous Enzyme Family.
Chem. Biol. Drug Des. V. 79 128 2012
PubMed-ID: 22039970  |  Reference-DOI: 10.1111/J.1747-0285.2011.01267.X

(-) Compounds

Molecule 1 - ASPARTATE-SEMIALDEHYDE DEHYDROGENASE
    Chains: A, B
    EC Number: 1.2.1.11
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET 28A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLAZMID
    Gene: CGSSP23BS72_03388
    Organism Scientific: STREPTOCOCCUS PNEUMONIAE
    Organism Taxid: 406563
    Strain: SP23-BS72

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 14)

Asymmetric/Biological Unit (4, 14)
No.NameCountTypeFull Name
125A2Ligand/Ion5'-O-MONOPHOSPHORYLADENYLYL(2'->5')ADENYLYL(2'->5')ADENOSINE
2EDO8Ligand/Ion1,2-ETHANEDIOL
3L142Ligand/IonTRANS-CYCLOHEXANE-1,4-DICARBOXYLIC ACID
4NA2Ligand/IonSODIUM ION

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLY A:9 , THR A:11 , GLY A:12 , ALA A:13 , ALA A:36 , SER A:37 , ARG A:39 , SER A:40 , THR A:57 , ALA A:72 , THR A:76 , GLY A:161 , MET A:162 , HOH A:451 , HOH A:544 , HOH A:548 , HOH A:639 , HOH A:711 , HOH A:1212BINDING SITE FOR RESIDUE 25A A 367
02AC2SOFTWAREGLY B:9 , THR B:11 , GLY B:12 , ALA B:13 , ALA B:36 , SER B:37 , ARG B:39 , SER B:40 , THR B:57 , ALA B:72 , THR B:76 , GLY B:161 , MET B:162 , HOH B:447 , HOH B:536 , HOH B:600 , HOH B:603 , HOH B:604 , HOH B:625 , HOH B:628 , HOH B:718BINDING SITE FOR RESIDUE 25A B 367
03AC3SOFTWARESER A:96 , ARG A:99 , GLY A:159 , ALA A:160 , GLU A:220 , LYS A:223 , ARG A:245 , HOH A:589 , HOH A:1220BINDING SITE FOR RESIDUE L14 A 368
04AC4SOFTWARESER B:96 , ARG B:99 , ASN B:127 , GLY B:159 , ALA B:160 , GLU B:220 , LYS B:223 , ARG B:245 , HOH B:653 , HOH B:888 , HOH B:1237BINDING SITE FOR RESIDUE L14 B 368
05AC5SOFTWARETHR A:26 , EDO A:369 , HOH A:592 , GLU B:24 , SER B:25 , TRP B:332 , GLU B:339 , HOH B:446 , HOH B:587BINDING SITE FOR RESIDUE EDO B 369
06AC6SOFTWAREGLU A:24 , SER A:25 , TRP A:332 , GLU A:339 , HOH A:376 , HOH A:498 , HOH A:592 , THR B:26 , EDO B:369BINDING SITE FOR RESIDUE EDO A 369
07AC7SOFTWARESER A:250 , GLY A:298 , ASP A:324 , LEU A:326 , HOH A:555 , HOH A:950BINDING SITE FOR RESIDUE EDO A 370
08AC8SOFTWARESER B:250 , GLY B:298 , ASP B:324 , LEU B:326 , HOH B:466BINDING SITE FOR RESIDUE EDO B 370
09AC9SOFTWAREASP A:312 , HOH A:497 , HOH A:1319 , LYS B:229BINDING SITE FOR RESIDUE EDO A 371
10BC1SOFTWAREGLY A:2 , PRO A:28 , HOH B:436 , HOH B:1204BINDING SITE FOR RESIDUE EDO B 371
11BC2SOFTWARELYS A:229 , ASP B:312 , HOH B:416BINDING SITE FOR RESIDUE EDO B 372
12BC3SOFTWAREHOH A:402 , GLY B:2 , HOH B:1121BINDING SITE FOR RESIDUE EDO A 372
13BC4SOFTWAREILE A:273 , ALA A:274 , PHE A:276 , ALA A:279 , GLU B:343 , HOH B:613BINDING SITE FOR RESIDUE NA A 373
14BC5SOFTWAREASP B:147 , SER B:236 , HOH B:474 , HOH B:914 , HOH B:939BINDING SITE FOR RESIDUE NA B 373

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3PWK)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Leu A:190 -Pro A:191
2Leu B:190 -Pro B:191

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3PWK)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3PWK)

(-) Exons   (0, 0)

(no "Exon" information available for 3PWK)

(-) 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:357
                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains d3pwka1 A:2-127,A:330-358 Aspartate beta-semialdehyde dehydrogenase                                                           d3pwka2 A:128-329 Aspartate beta-semialdehyde dehydrogenase                                                                                                                                               d3pwka1 A:2-127,A:330-358     SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee...hhhhhhhhhhhhh....eeeeeeee.......eeee..eeeeeee..........eeee..hhhhhhhhhhhhhhh..eeee..............hhhhhhhhhh....eee..hhhhhhhhhhhhhhhhhhh..eeeeeee.hhhhhhhhhhhhhhhhhhhhhhhh.hhhhh................................hhhhhhhhhhhhhhh.....eeeee.........eeeeeeee.....hhhhhhhhhhhh..eee..hhhhh...hhhhhh....eeeeeeee......eeeeeeee......hhhhhhhhhhhhhhh.............. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pwk A   2 GYTVAVVGATGAVGAQMIKMLEESTLPIDKIRYLASARSAGKSLKFKDQDITIEETTETAFEGVDIALFSAGSSTSAKYAPYAVKAGVVVVDNTSYFRQNPDVPLVVPEVNAHALDAHNGIIACPNCSTIQMMVALEPVRQKWGLDRIIVSTYQAVSGAGMGAILETQRELREVLNDGVKPCDLHAEILPSGGDKKHYPIAFNALPQIDVFTDNDYTYEEMKMTKETKKIMEDDSIAVSATCVRIPVLSAHSESVYIETKEVAPIEEVKAAIAAFPGAVLEDDVAHQIYPQAINAVGSRDTFVGRIRKDLDAEKGIHMWVVSDNLLKGAAWNSVQIAETLHERGLVRPTAELKFELK 358
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       


Chain B from PDB  Type:PROTEIN  Length:359
                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains d3pwkb1 B:2-127,B:330-360 Aspartate beta-semialdehyde dehydrogenase                                                           d3pwkb2 B:128-329 Aspartate beta-semialdehyde dehydrogenase                                                                                                                                               d3pwkb1 B:2-127,B:330-360       SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee...hhhhhhhhhhhhh....eeeeeeee.......eeee..eeeeeee..........eeee..hhhhhhhhhhhhhhhh.eeee..............hhhhhhhhhhhh..eee..hhhhhhhhhhhhhhhhhhh..eeeeeee.hhhhhhhhhhhhhhhhhhhhhhhh.hhhhh................................hhhhhhhhhhhhhhh.....eeeee.........eeeeeeee.....hhhhhhhhhhh...eee..hhhhh...hhhhhh....eeeeeeee......eeeeeeee......hhhhhhhhhhhhhhh................ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pwk B   2 GYTVAVVGATGAVGAQMIKMLEESTLPIDKIRYLASARSAGKSLKFKDQDITIEETTETAFEGVDIALFSAGSSTSAKYAPYAVKAGVVVVDNTSYFRQNPDVPLVVPEVNAHALDAHNGIIACPNCSTIQMMVALEPVRQKWGLDRIIVSTYQAVSGAGMGAILETQRELREVLNDGVKPCDLHAEILPSGGDKKHYPIAFNALPQIDVFTDNDYTYEEMKMTKETKKIMEDDSIAVSATCVRIPVLSAHSESVYIETKEVAPIEEVKAAIAAFPGAVLEDDVAHQIYPQAINAVGSRDTFVGRIRKDLDAEKGIHMWVVSDNLLKGAAWNSVQIAETLHERGLVRPTAELKFELKLE 360
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351
   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  (2, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3PWK)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3PWK)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3PWK)

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 Related Entries

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(-) Related Entries Specified in the PDB File

2gz2 THE SAME PROTEIN COMPLEXED ONLY WITH 2',5'-ADP
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3q0e
3q11
3q1l