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(-) Description

Title :  CRYSTAL COMPLEX STRUCTURE OF SP-ASPARTATE-SEMIALDEHYDE-DEHYDROGENASE WITH NICOTINAMIDE ADENINE DINUCLEOTIDE PHOSPHATE AND PHTHALIC ACID
 
Authors :  A. G. Pavlovsky, R. E. Viola
Date :  20 Aug 14  (Deposition) - 10 Dec 14  (Release) - 31 Dec 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.81
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Rossmann Fold, Dehydrogenase, Oxidoreductase, Nadp (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
    Fragment: ASPARTATE-SEMIALDEHYDE-DEHYDROGENASE
    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, 17)

Asymmetric/Biological Unit (5, 17)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2EDO9Ligand/Ion1,2-ETHANEDIOL
3NA3Ligand/IonSODIUM ION
4NAP2Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
5PHT1Ligand/IonPHTHALIC ACID

(-) Sites  (17, 17)

Asymmetric Unit (17, 17)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREILE A:273 , ALA A:274 , PHE A:276 , ALA A:279 , GLU B:343 , HOH B:599BINDING SITE FOR RESIDUE NA A 401
02AC2SOFTWAREGLU A:343 , ILE B:273 , ALA B:274 , PHE B:276 , ALA B:279 , HOH B:624BINDING SITE FOR RESIDUE NA A 402
03AC3SOFTWARESER A:74 , THR A:95 , SER A:96 , ARG A:99 , ASN A:127 , GLY A:159 , LYS A:223 , NAP A:404 , ACT A:411BINDING SITE FOR RESIDUE PHT A 403
04AC4SOFTWAREGLY A:9 , THR A:11 , GLY A:12 , ALA A:13 , VAL A:14 , ALA A:36 , SER A:37 , ARG A:39 , SER A:40 , THR A:57 , SER A:71 , ALA A:72 , GLY A:73 , ASN A:94 , THR A:95 , ARG A:99 , PRO A:126 , ASN A:127 , CYS A:128 , GLY A:161 , MET A:162 , GLY A:329 , PHT A:403 , ACT A:411 , HOH A:578 , HOH A:579 , HOH A:592 , HOH A:617 , HOH A:634 , HOH A:643 , HOH A:649BINDING SITE FOR RESIDUE NAP A 404
05AC5SOFTWAREGLU A:24 , SER A:25 , TRP A:332 , GLU A:339 , HOH A:503 , THR B:26BINDING SITE FOR RESIDUE EDO A 405
06AC6SOFTWARESER A:250 , GLY A:298 , ASP A:324 , LEU A:326 , HOH A:582BINDING SITE FOR RESIDUE EDO A 406
07AC7SOFTWARELEU A:311 , ASP A:312 , HOH A:560 , LYS B:229BINDING SITE FOR RESIDUE EDO A 407
08AC8SOFTWAREGLU A:282 , PRO A:291 , GLN A:292 , ASN A:295 , PHE A:303 , EDO A:409BINDING SITE FOR RESIDUE EDO A 408
09AC9SOFTWAREGLN A:288 , ILE A:289 , TYR A:290 , GLN A:292 , ASN A:295 , EDO A:408 , TYR B:199BINDING SITE FOR RESIDUE EDO A 409
10BC1SOFTWAREASN A:127 , CYS A:128 , GLN A:155 , GLY A:159 , GLU A:220 , ARG A:245 , HIS A:252 , ACT A:411 , HOH A:641BINDING SITE FOR RESIDUE ACT A 410
11BC2SOFTWARECYS A:128 , GLN A:155 , GLY A:159 , ARG A:245 , HIS A:252 , PHT A:403 , NAP A:404 , ACT A:410BINDING SITE FOR RESIDUE ACT A 411
12BC3SOFTWAREASP B:147 , SER B:236 , HOH B:551 , HOH B:561 , HOH B:612BINDING SITE FOR RESIDUE NA B 401
13BC4SOFTWAREGLY B:9 , THR B:11 , GLY B:12 , ALA B:13 , ALA B:36 , SER B:37 , ARG B:39 , SER B:40 , LYS B:43 , THR B:57 , ALA B:72 , THR B:76 , GLY B:161 , MET B:162 , GLY B:163 , HOH B:580 , HOH B:596 , HOH B:633BINDING SITE FOR RESIDUE NAP B 402
14BC5SOFTWAREALA B:238BINDING SITE FOR RESIDUE EDO B 403
15BC6SOFTWARESER B:250 , GLY B:298 , ASP B:324 , LEU B:326 , HOH B:550BINDING SITE FOR RESIDUE EDO B 404
16BC7SOFTWAREGLU B:282 , PRO B:291 , GLN B:292 , ASN B:295 , PHE B:303 , HOH B:513BINDING SITE FOR RESIDUE EDO B 405
17BC8SOFTWARELYS A:229 , ASP B:312 , HOH B:529BINDING SITE FOR RESIDUE EDO B 406

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4R51)

(-) 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 4R51)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4R51)

(-) Exons   (0, 0)

(no "Exon" information available for 4R51)

(-) 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:360
                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ 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
                 4r51 A   2 GYTVAVVGATGAVGAQMIKMLEESTLPIDKIRYLASARSAGKSLKFKDQDITIEETTETAFEGVDIALFSAGSSTSAKYAPYAVKAGVVVVDNTSYFRQNPDVPLVVPEVNAHALDAHNGIIACPNCSTIQMMVALEPVRQKWGLDRIIVSTYQAVSGAGMGAILETQRELREVLNDGVKPCDLHAEILPSGGDKKHYPIAFNALPQIDVFTDNDYTYEEMKMTKETKKIMEDDSIAVSATCVRIPVLSAHSESVYIETKEVAPIEEVKAAIAAFPGAVLEDDVAHQIYPQAINAVGSRDTFVGRIRKDLDAEKGIHMWVVSDNLLKGAAWNSVQIAETLHERGLVRPTAELKFELKLEH 361
                                    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       361


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.......eeee..eeeeeee..........eeee..hhhhhhhhhhhhhhh..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
                 4r51 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 4R51)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4R51)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4R51)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 4R51)

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 Related Entries

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(-) Related Entries Specified in the PDB File

4r3n 4r3w 4r41 4r4j