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(-) Description

Title :  COMPLEX CRYSTAL STRUCTURE OF 4-NITRO-2-PHOSPHONO-BENZOIC ACID WITH SP-ASPARTATE-SEMIALDEHYDE DEHYDROGENASE AND NICOTINAMIDE-DINUCLEOTIDE
 
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 :  1.61
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Rossmann Fold, 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: 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, 16)

Asymmetric/Biological Unit (5, 16)
No.NameCountTypeFull Name
14NO2Ligand/Ion4-NITRO-2-PHOSPHONOBENZOIC ACID
2ACT1Ligand/IonACETATE ION
3EDO8Ligand/Ion1,2-ETHANEDIOL
4NA3Ligand/IonSODIUM ION
5NAP2Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

(-) Sites  (16, 16)

Asymmetric Unit (16, 16)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREVAL A:14 , SER A:71 , ALA A:72 , GLY A:73 , SER A:74 , ASN A:94 , THR A:95 , SER A:96 , ARG A:99 , ASN A:127 , LYS A:223BINDING SITE FOR RESIDUE 4NO A 401
02AC2SOFTWAREGLY 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 , GLY A:161 , MET A:162 , GLY A:163 , LEU A:166 , HOH A:598 , HOH A:648BINDING SITE FOR RESIDUE NAP A 402
03AC3SOFTWAREVAL A:111 , HIS A:114 , ILE A:231 , MET A:232BINDING SITE FOR RESIDUE ACT A 403
04AC4SOFTWAREILE A:273 , ALA A:274 , PHE A:276 , ALA A:279 , HOH A:614 , GLU B:343BINDING SITE FOR RESIDUE NA A 404
05AC5SOFTWAREGLU A:343 , HOH A:632 , ILE B:273 , ALA B:274 , PHE B:276 , ALA B:279BINDING SITE FOR RESIDUE NA A 405
06AC6SOFTWARESER A:250 , GLY A:298 , ASP A:324 , LEU A:326 , LEU A:327 , HOH A:585BINDING SITE FOR RESIDUE EDO A 406
07AC7SOFTWAREGLU A:282 , PRO A:291 , GLN A:292 , ASN A:295 , ALA A:296 , PHE A:303BINDING SITE FOR RESIDUE EDO A 407
08AC8SOFTWARELYS A:229 , ASP B:312 , HOH B:534BINDING SITE FOR RESIDUE EDO A 408
09AC9SOFTWAREGLU A:24 , SER A:25 , TRP A:332 , GLU A:339 , HOH A:503BINDING SITE FOR RESIDUE EDO A 409
10BC1SOFTWARELEU A:311 , ASP A:312 , HOH A:561 , LYS B:229BINDING SITE FOR RESIDUE EDO A 410
11BC2SOFTWARESER B:71 , ALA B:72 , GLY B:73 , SER B:74 , ASN B:94 , SER B:96 , ARG B:99 , ASN B:127 , LYS B:223BINDING SITE FOR RESIDUE 4NO B 401
12BC3SOFTWAREGLY 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:587 , HOH B:606 , HOH B:611BINDING SITE FOR RESIDUE NAP B 402
13BC4SOFTWAREASP B:147 , SER B:236 , HOH B:558 , HOH B:567 , HOH B:619BINDING SITE FOR RESIDUE NA B 403
14BC5SOFTWARESER B:250 , GLY B:298 , ASP B:324 , LEU B:326 , HOH B:555BINDING SITE FOR RESIDUE EDO B 404
15BC6SOFTWAREGLU B:282 , PRO B:291 , GLN B:292 , ASN B:295 , PHE B:303 , HOH B:518BINDING SITE FOR RESIDUE EDO B 405
16BC7SOFTWAREASP A:312 , ARG B:148 , HOH B:567BINDING SITE FOR RESIDUE EDO B 406

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4R41)

(-) 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 4R41)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4R41)

(-) Exons   (0, 0)

(no "Exon" information available for 4R41)

(-) 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..eeeeeee.hhhhhhhhhhhhhhhhhhhhhhhh.hhhhh................................hhhhhhhhhhhhhhh.....eeeee.........eeeeeeee.....hhhhhhhhhhh...eee..hhhhh...hhhhhh....eeeeeeee......eeeeeeee......hhhhhhhhhhhhhhh.............. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4r41 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..eeeeeee.hhhhhhhhhhhhhhhhhhhhhhhh.hhhhh................................hhhhhhhhhhhhhhh.....eeeee.........eeeeeeee.....hhhhhhhhhhhh..eee..hhhhh...hhhhhh....eeeeeeee......eeeeeeee......hhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4r41 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 4R41)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4R41)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4R41)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 4R41)

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  4r41
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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 4r3w 4r4j 4r51 4r54 4r5h 4r5m