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(-) Description

Title :  CRYSTAL STRUCTURE OF THE TERNARY COMPLEX OF SP-ASADH WITH NADP AND 1, 2,3-BENZENETRICARBOXYLIC ACID
 
Authors :  A. G. Pavlovsky, R. E. Viola
Date :  16 Aug 14  (Deposition) - 10 Dec 14  (Release) - 31 Dec 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.35
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Protein-Nadp-Ligand Complex, Dehydrogenase, Oxidoreductase, Nadp Binding (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: PER28A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: ASD
    Organism Scientific: STREPTOCOCCUS PNEUMONIAE
    Organism Taxid: 1313
    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
13GQ2Ligand/IonBENZENE-1,2,3-TRICARBOXYLIC ACID
2ACT4Ligand/IonACETATE ION
3EDO5Ligand/Ion1,2-ETHANEDIOL
4NA3Ligand/IonSODIUM ION
5NAP3Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

(-) 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:609BINDING SITE FOR RESIDUE NA A 401
02AC2SOFTWAREGLU A:343 , ILE B:273 , ALA B:274 , PHE B:276 , ALA B:279 , HOH B:645BINDING SITE FOR RESIDUE NA A 402
03AC3SOFTWAREGLY 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 , 3GQ A:404 , HOH A:586 , HOH A:587 , HOH A:603 , HOH A:631 , HOH A:646 , HOH A:669 , HOH A:679BINDING SITE FOR RESIDUE NAP A 403
04AC4SOFTWARESER A:74 , THR A:95 , SER A:96 , ARG A:99 , ASN A:127 , LYS A:223 , NAP A:403 , ACT A:407BINDING SITE FOR RESIDUE 3GQ A 404
05AC5SOFTWAREGLU A:24 , SER A:25 , ARG A:300 , TRP A:332 , GLU A:339 , HOH A:503 , THR B:26 , EDO B:405BINDING SITE FOR RESIDUE EDO A 405
06AC6SOFTWAREASN A:127 , CYS A:128 , GLN A:155 , GLY A:159 , GLU A:220 , ARG A:245 , HIS A:252 , ACT A:407 , HOH A:663BINDING SITE FOR RESIDUE ACT A 406
07AC7SOFTWARECYS A:128 , GLN A:155 , GLY A:159 , ILE A:209 , ARG A:245 , HIS A:252 , 3GQ A:404 , ACT A:406 , HOH A:663BINDING SITE FOR RESIDUE ACT A 407
08AC8SOFTWAREASP B:147 , SER B:236 , HOH B:551 , HOH B:562 , HOH B:628BINDING SITE FOR RESIDUE NA B 401
09AC9SOFTWAREGLY 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 , NAP B:403 , HOH B:585 , HOH B:604 , HOH B:605 , HOH B:614 , HOH B:650BINDING SITE FOR RESIDUE NAP B 402
10BC1SOFTWAREGLY B:9 , THR B:11 , GLY B:12 , ALA B:13 , VAL B:14 , ALA B:36 , SER B:37 , SER B:40 , THR B:57 , SER B:71 , ALA B:72 , GLY B:73 , THR B:76 , ASN B:94 , THR B:95 , PRO B:126 , ASN B:127 , CYS B:128 , GLY B:159 , GLY B:161 , MET B:162 , GLY B:329 , NAP B:402 , 3GQ B:404 , HOH B:585 , HOH B:588 , HOH B:613 , HOH B:616 , HOH B:635 , HOH B:650 , HOH B:656BINDING SITE FOR RESIDUE NAP B 403
11BC2SOFTWARESER B:74 , THR B:95 , SER B:96 , ARG B:99 , ASN B:127 , GLY B:159 , LYS B:223 , NAP B:403 , ACT B:410 , HOH B:635BINDING SITE FOR RESIDUE 3GQ B 404
12BC3SOFTWARETHR A:26 , EDO A:405 , GLU B:24 , SER B:25 , ARG B:300 , TRP B:332 , GLU B:339 , HOH B:540BINDING SITE FOR RESIDUE EDO B 405
13BC4SOFTWARESER B:250 , GLY B:298 , ASP B:324 , LEU B:326 , HOH B:549BINDING SITE FOR RESIDUE EDO B 406
14BC5SOFTWAREGLU B:282 , PRO B:291 , GLN B:292 , ASN B:295 , PHE B:303 , HOH B:510BINDING SITE FOR RESIDUE EDO B 407
15BC6SOFTWARELYS A:229 , ASP B:312 , HOH B:527BINDING SITE FOR RESIDUE EDO B 408
16BC7SOFTWAREASN B:127 , CYS B:128 , GLN B:155 , GLY B:159 , GLU B:220 , ARG B:245 , HIS B:252 , ACT B:410BINDING SITE FOR RESIDUE ACT B 409
17BC8SOFTWAREASN B:127 , CYS B:128 , GLN B:155 , GLY B:159 , ILE B:209 , ARG B:245 , HIS B:252 , 3GQ B:404 , ACT B:409BINDING SITE FOR RESIDUE ACT B 410

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4R3N)

(-) 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 4R3N)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4R3N)

(-) Exons   (0, 0)

(no "Exon" information available for 4R3N)

(-) 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..hhhhhhhhhhhhhhh..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
                 4r3n 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.......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
                 4r3n 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 4R3N)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4R3N)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4R3N)

(-) Gene Ontology  (18, 18)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        Q8DQ00_STRR6 | Q8DQ00: 2gyy 2gz1 2gz2 2gz3
UniProtKB/TrEMBL
        Q8DQ00_STRR6 | Q8DQ00: 3q1l

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4R3N)