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(-) Description

Title :  CRYSTAL STRUCTURE ANALYSIS OF THE 1,2,3-TRICARBOXYLATE BENZOIC ACID BOUND TO SP-ASADH-2'5'-ADP COMPLEX
 
Authors :  A. G. Pavlovsky, R. E. Viola
Date :  18 Aug 14  (Deposition) - 10 Dec 14  (Release) - 31 Dec 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.91
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Dehydrogenase, Nicotineamid-Dinucleotide, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. G. Pavlovsky, B. Thangavelu, P. Bhansali, R. E. Viola
A Cautionary Tale Of Structure-Guided Inhibitor Development Against An Essential Enzyme In The Aspartate-Biosynthetic Pathway.
Acta Crystallogr. , Sect. D V. 70 3244 2014
PubMed-ID: 25478842  |  Reference-DOI: 10.1107/S1399004714023979

(-) Compounds

Molecule 1 - ASPARTATE-SEMIALDEHYDE DEHYDROGENASE
    Chains: A, B
    EC Number: 1.2.1.11
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: ASD, CGSSP23BS72_03388
    Organism Scientific: STREPTOCOCCUS PNEUMONIAE
    Organism Taxid: 406563
    Strain: SP23-BS72
    Synonym: ASA DEHYDROGENASE, ASADH, ASPARTATE-BETA-SEMIALDEHYDE DEHYDROGENASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 14)

Asymmetric/Biological Unit (5, 14)
No.NameCountTypeFull Name
13GQ1Ligand/IonBENZENE-1,2,3-TRICARBOXYLIC ACID
2A2P2Ligand/IonADENOSINE-2'-5'-DIPHOSPHATE
3ACT1Ligand/IonACETATE ION
4EDO7Ligand/Ion1,2-ETHANEDIOL
5NA3Ligand/IonSODIUM ION

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREILE A:273 , ALA A:274 , PHE A:276 , ALA A:279 , GLU B:343 , HOH B:569BINDING SITE FOR RESIDUE NA A 401
02AC2SOFTWAREGLY A:73 , SER A:74 , THR A:95 , SER A:96 , ARG A:99 , ASN A:127 , GLY A:159 , LYS A:223BINDING SITE FOR RESIDUE 3GQ A 402
03AC3SOFTWAREGLU A:24 , SER A:25 , TRP A:332 , GLU A:339 , HOH A:503 , EDO B:404BINDING SITE FOR RESIDUE EDO A 403
04AC4SOFTWARESER A:250 , GLY A:298 , ASP A:324 , LEU A:326 , LEU A:327BINDING SITE FOR RESIDUE EDO A 404
05AC5SOFTWAREASN A:127 , CYS A:128 , GLN A:155 , GLY A:159 , GLU A:220 , ARG A:245 , HIS A:252BINDING SITE FOR RESIDUE ACT A 405
06AC6SOFTWAREGLY 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:580 , HOH A:583 , HOH A:595BINDING SITE FOR RESIDUE A2P A 406
07AC7SOFTWAREGLU A:343 , ILE B:273 , ALA B:274 , PHE B:276 , ALA B:279 , HOH B:573BINDING SITE FOR RESIDUE NA B 401
08AC8SOFTWAREASP B:147 , SER B:236 , HOH B:574BINDING SITE FOR RESIDUE NA B 402
09AC9SOFTWARELEU A:311 , ASP A:312 , THR B:225 , LYS B:229BINDING SITE FOR RESIDUE EDO B 403
10BC1SOFTWAREEDO A:403 , GLU B:24 , SER B:25 , TRP B:332 , GLU B:339 , HOH B:533BINDING SITE FOR RESIDUE EDO B 404
11BC2SOFTWARESER B:250 , GLY B:298 , ASP B:324 , LEU B:326BINDING SITE FOR RESIDUE EDO B 405
12BC3SOFTWAREGLU B:282 , PRO B:291 , GLN B:292 , ASN B:295 , ALA B:296 , PHE B:303BINDING SITE FOR RESIDUE EDO B 406
13BC4SOFTWARELYS A:229 , LEU B:311 , ASP B:312 , HOH B:523BINDING SITE FOR RESIDUE EDO B 407
14BC5SOFTWAREGLY B:9 , THR B:11 , GLY B:12 , ALA B:13 , ALA B:36 , SER B:37 , SER B:40 , THR B:57 , ALA B:72 , THR B:76 , GLY B:161 , MET B:162 , HOH B:567BINDING SITE FOR RESIDUE A2P B 408

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4R3W)

(-) 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 4R3W)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4R3W)

(-) Exons   (0, 0)

(no "Exon" information available for 4R3W)

(-) 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 --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee...hhhhhhhhhhhhh....eeeeeeee.......eeee..eeeeeee..........eeee..hhhhhhhhhhhhhhhh.eeee..............hhhhhhhhhhhh..eee..hhhhhhhhhhhhhhhhhhh..eeeeeeeehhhhhhhhhhhhhhhhhhhhhhhh.hhhhh................................hhhhhhhhhhhhhhhh....eeeeeeee......eeeeeeee.....hhhhhhhhhhhh..eee..hhhhh...hhhhhh....eeeeeeee......eeeeeeee......hhhhhhhhhhhhhhh.............. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4r3w 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:347
                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee...hhhhhhhhhhhhh....eeeeeeee.......eee....eee.ee..........eeee.hhhhhhhhhhhhhhhh..eeee..............hhhhhhhhhhhh..eee..hhhhhhhhhhhhhhhhhhh..eeeeeeeehhhhhhhhhhhhhhhhhhhhhhhh.hhhhh................................hhhhhhhhhhhhhhh.....eeeeeeee......eeeeeeee.....hhhhhhhhhhhh..eee..hhhhh...hhhhhh....eeeeeeee......eeeeeeee......hhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4r3w B   2 GYTVAVVGATGAVGAQMIKMLEESTLPIDKIRYLASARSAGKSLKFKDQDITIEETTETAFEGVDIALFSAGSSTSAKYAPYAVKAGVVVVDNTSYFRQNPDVPLVVPEVNAHALDAHNGIIACPNCSTIQMMVALEPVRQKWGLDRIIVSTYQAVSGAGMGAILETQRELREVLNDGVKPCDLHAEILPSGGDKKHYPIAFNALPQIDVFTDNDYTYEEMKMTKETKKIMEDDSIAVSATCVRIPVLSAHSESVYIETKEVAPIEEVKAAIAAFPGAVLEDDVAHQIYPQAINAVGSRDTFVGRIRKDLDAEKGIHMWVVSDNLLKGAAWNSVQIAETLHERGLVR 348
                                    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
   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 4R3W)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4R3W)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4R3W)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 4R3W)

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  1.2.1.11
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

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(-) Related Entries Specified in the PDB File

4r3n 1,2,3-TRICARBOXYLATE-BENZOIC ACID SP-ASADH-NADP COMPLEX
4r41
4r4j
4r51
4r54
4r5h
4r5m