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(-) Description

Title :  CRYSTALS STRUCTURE OF ASPARTATE BETA-SEMIALDEHYDE DEHYDROGENASE FROM STREPTOCOCCUS PNEUMONIAE WITH NADP AND ASPARTYL BETA-DIFLUOROPHOSPHONATE
 
Authors :  A. G. Pavlovsky, R. E. Viola, C. R. Faehnle
Date :  16 Dec 10  (Deposition) - 04 Jan 12  (Release) - 04 Jan 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Nadp, 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: PLASMID
    Gene: CGSSP23BS72_03388
    Organism Scientific: STREPTOCOCCUS PNEUMONIAE
    Organism Taxid: 1313

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 10)

Asymmetric/Biological Unit (4, 10)
No.NameCountTypeFull Name
1EDO5Ligand/Ion1,2-ETHANEDIOL
2NA1Ligand/IonSODIUM ION
3NAP2Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
4P4F2Ligand/Ion5,5-DIFLUORO-4-OXO-5-PHOSPHONO-D-NORVALINE

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
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 , GLY A:163 , HOH A:644 , HOH A:653 , HOH A:727 , HOH A:816BINDING SITE FOR RESIDUE NAP 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 , ALA B:72 , THR B:76 , ALA B:160 , GLY B:161 , MET B:162 , GLY B:163 , LEU B:166 , HOH B:447 , HOH B:631 , HOH B:649BINDING SITE FOR RESIDUE NAP B 367
03AC3SOFTWAREASN A:94 , ARG A:99 , ASN A:127 , CYS A:128 , GLN A:155 , GLY A:159 , ILE A:209 , GLU A:220 , LYS A:223 , ARG A:245 , HIS A:252BINDING SITE FOR RESIDUE P4F A 368
04AC4SOFTWAREARG B:99 , ASN B:127 , CYS B:128 , GLN B:155 , GLY B:159 , ILE B:209 , GLU B:220 , LYS B:223 , ARG B:245 , HIS B:252BINDING SITE FOR RESIDUE P4F B 368
05AC5SOFTWAREGLU A:343 , ALA B:274 , PHE B:276 , ALA B:279 , HOH B:698BINDING SITE FOR RESIDUE NA A 369
06AC6SOFTWARETHR A:26 , EDO A:370 , GLU B:24 , SER B:25 , TRP B:332 , GLU B:339 , HOH B:387 , HOH B:446 , HOH B:526BINDING SITE FOR RESIDUE EDO B 369
07AC7SOFTWAREGLU A:24 , SER A:25 , TRP A:332 , GLU A:339 , HOH A:439 , HOH A:481 , THR B:26 , EDO B:369 , HOH B:526BINDING SITE FOR RESIDUE EDO A 370
08AC8SOFTWARESER A:250 , GLY A:298 , ASP A:324 , LEU A:326 , HOH A:377BINDING SITE FOR RESIDUE EDO A 371
09AC9SOFTWARESER B:250 , GLY B:298 , ASP B:324 , LEU B:326 , HOH B:532BINDING SITE FOR RESIDUE EDO B 370
10BC1SOFTWARELEU A:311 , ASP A:312 , HOH A:415 , LYS B:229BINDING SITE FOR RESIDUE EDO A 372

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3Q11)

(-) 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 3Q11)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3Q11)

(-) Exons   (0, 0)

(no "Exon" information available for 3Q11)

(-) 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:358
                                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains d3q11a1 A:2-127,A:330-359 Aspartate beta-semialdehyde dehydrogenase                                                           d3q11a2 A:128-329 Aspartate beta-semialdehyde dehydrogenase                                                                                                                                               d3q11a1 A:2-127,A:330-359      SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee...hhhhhhhhhhhhh....eeeeeeee.......eeee..eeee.ee..........eeee.hhhhhhhhhhhhhhhhh.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
                 3q11 A   2 GYTVAVVGATGAVGAQMIKMLEESTLPIDKIRYLASARSAGKSLKFKDQDITIEETTETAFEGVDIALFSAGSSTSAKYAPYAVKAGVVVVDNTSYFRQNPDVPLVVPEVNAHALDAHNGIIACPNCSTIQMMVALEPVRQKWGLDRIIVSTYQAVSGAGMGAILETQRELREVLNDGVKPCDLHAEILPSGGDKKHYPIAFNALPQIDVFTDNDYTYEEMKMTKETKKIMEDDSIAVSATCVRIPVLSAHSESVYIETKEVAPIEEVKAAIAAFPGAVLEDDVAHQIYPQAINAVGSRDTFVGRIRKDLDAEKGIHMWVVSDNLLKGAAWNSVQIAETLHERGLVRPTAELKFELKL 359
                                    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:357
                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains d3q11b1 B:2-127,B:330-358 Aspartate beta-semialdehyde dehydrogenase                                                           d3q11b2 B:128-329 Aspartate beta-semialdehyde dehydrogenase                                                                                                                                               d3q11b1 B:2-127,B:330-358     SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee...hhhhhhhhhhhhh....eeeeeeee.......eeee..eeeeeee..........eeee..hhhhhhhhhhhhhhh..eeee..............hhhhhhhhhhhh..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
                 3q11 B   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
   Legend:   → Mismatch (orange background)
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    → 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 3Q11)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3Q11)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3Q11)

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  1.2.1.11
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 Related Entries

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(-) Related Entries Specified in the PDB File

3pyx 3pzb 3pzr 3q0e 3q1l