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(-) Description

Title :  CRYSTAL STRUCTURE OF 3-DEHYDROQUINATE SYNTHASE (DHQS) IN COMPLEX WITH ZN2+ AND CARBAPHOSPHONATE
 
Authors :  C. E. Nichols, J. Ren, H. K. Lamb, A. R. Hawkins, D. K. Stammers
Date :  03 Feb 03  (Deposition) - 18 Mar 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.51
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Shikimate Pathway, Aromatic Amino Acid Biosynthesis, Dhqs, Open Form, Form B, Domain Movement, Cyclase, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. E. Nichols, J. Ren, H. K. Lamb, A. R. Hawkins, D. K. Stammers
Ligand-Induced Conformational Changes And A Mechanism For Domain Closure In Aspergillus Nidulans Dehydroquinate Synthase
J. Mol. Biol. V. 327 129 2003
PubMed-ID: 12614613  |  Reference-DOI: 10.1016/S0022-2836(03)00086-X
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 3-DEHYDROQUINATE SYNTHASE
    ChainsA, B
    EC Number4.2.3.4
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPTR51
    Expression System StrainGLW38 (AROB-)
    Expression System Taxid562
    Expression System VectorPTRC99A
    Expression System Vector TypePLASMID
    GeneAROMA
    Organism ScientificEMERICELLA NIDULANS
    Organism Taxid162425
    SynonymDHQS

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric/Biological Unit (3, 5)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2CRB2Ligand/Ion[1R-(1ALPHA,3BETA,4ALPHA,5BETA)]-5-(PHOSPHONOMETHYL)-1,3,4-TRIHYDROXYCYCLOHEXANE-1-CARBOXYLIC ACID
3ZN2Ligand/IonZINC ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU B:194 , HIS B:271 , HIS B:287 , CRB B:501BINDING SITE FOR RESIDUE ZN B 601
2AC2SOFTWAREGLU A:194 , HIS A:271 , HIS A:287 , CRB A:500BINDING SITE FOR RESIDUE ZN A 600
3AC3SOFTWARELYS A:89 , HOH A:616 , LYS B:89BINDING SITE FOR RESIDUE CL A 602
4AC4SOFTWAREASP A:146 , LYS A:152 , ASN A:162 , GLU A:194 , LYS A:197 , LYS A:250 , ARG A:264 , LEU A:267 , ASN A:268 , HIS A:271 , HIS A:275 , HIS A:287 , LYS A:356 , ZN A:600 , HOH A:612 , HOH A:621 , ARG B:130BINDING SITE FOR RESIDUE CRB A 500
5AC5SOFTWAREARG A:130 , ASP B:146 , LYS B:152 , ASN B:162 , GLU B:194 , LYS B:197 , LYS B:250 , ARG B:264 , LEU B:267 , ASN B:268 , HIS B:271 , HIS B:275 , HIS B:287 , LYS B:356 , ZN B:601 , HOH B:614 , HOH B:617 , HOH B:864BINDING SITE FOR RESIDUE CRB B 501

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1NVD)

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1Thr A:67 -Pro A:68
2Asn A:100 -Pro A:101
3Thr A:282 -Pro A:283
4Thr B:67 -Pro B:68
5Asn B:100 -Pro B:101
6Thr B:282 -Pro B:283

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1NVD)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1NVD)

(-) Exons   (0, 0)

(no "Exon" information available for 1NVD)

(-) 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:385
 aligned with ARO1_EMENI | P07547 from UniProtKB/Swiss-Prot  Length:1583

    Alignment length:390
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393
           ARO1_EMENI     4 PTKISILGRESIIADFGLWRNYVAKDLISDCSSTTYVLVTDTNIGSIYTPSFEEAFRKAAAEITPSPRLLIYNAPPGEVSKSRQTKADIEDWMLSQNPPCGRDTVVIALGGGVIGDLTGFVASTYMRGVRYVQVPTTLLAMVDSSIGGKTAIDTPLGKNLIGAIWQPTKIYIDLEFLETLPVREFINGMAEVIKTAAISSEEEFTALEENAETILKAVRREVRPGEHRFEGIEEILKARILASARHKAYVVSADEREGGLRNLLNWGHSIGHAIEAILTPQILHGECVAIGMVKEAELARHLGILKGVAVSRIVKCLAAYGLPTSLKDARIRKLTAGKHCSVDQLMFNMALDKKNDGPKKKIVLLSAIGTPYETRASVVANEDIRVVLAP 393
               SCOP domains d1nvda_ A: Dehydroquinate synthase, DHQS                                                                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains 1nvdA01 A:4-182  [code=3.40.50.1970, no name defined]                                                                                                                              1nvdA02 A:183-391 Dehydroquinate synthase-l     ike - alpha domain                                                                                                                                               -- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeee..eeeeeee.hhhhhhhhhhhhhhh...eeeeeeehhhhhhhhhhhhhhhhhhhh......eeeeeee..hhhhhhhhhhhhhhhhhhh.........eeeeeehhhhhhhhhhhhhhhhhh.eeeeee.hhhhhhh.....eeeeee..eeeeeeee....eeeee.hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh..-----.hhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.......hhhhhhhhh....hhhhhhhhhh..........ee..eee..ee.....ee.hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1nvd A   4 PTKISILGRESIIADFGLWRNYVAKDLISDCSSTTYVLVTDTNIGSIYTPSFEEAFRKRAAEITPSPRLLIYNRPPGEVSKSRQTKADIEDWMLSQNPPCGRDTVVIALGGGVIGDLTGFVASTYMRGVRYVQVPTTLLAMVDSSIGGKTAIDTPLGKNLIGAIWQPTKIYIDLEFLETLPVREFINGMAEVIKTAAISSEEEFTALEENAETILKAVRREV-----RFEGTEEILKARILASARHKAYVVSADEREGGLRNLLNWGHSIGHAIEAILTPQILHGECVAIGMVKEAELARHLGILKGVAVSRIVKCLAAYGLPTSLKDARIRKLTAGKHCSVDQLMFNMALDKKNDGPKKKIVLLSAIGTPYETRASVVANEDIRVVLAP 393
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223 |     233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393
                                                                                                                                                                                                                                                       225   231                                                                                                                                                                  

Chain B from PDB  Type:PROTEIN  Length:382
 aligned with ARO1_EMENI | P07547 from UniProtKB/Swiss-Prot  Length:1583

    Alignment length:390
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393
           ARO1_EMENI     4 PTKISILGRESIIADFGLWRNYVAKDLISDCSSTTYVLVTDTNIGSIYTPSFEEAFRKAAAEITPSPRLLIYNAPPGEVSKSRQTKADIEDWMLSQNPPCGRDTVVIALGGGVIGDLTGFVASTYMRGVRYVQVPTTLLAMVDSSIGGKTAIDTPLGKNLIGAIWQPTKIYIDLEFLETLPVREFINGMAEVIKTAAISSEEEFTALEENAETILKAVRREVRPGEHRFEGIEEILKARILASARHKAYVVSADEREGGLRNLLNWGHSIGHAIEAILTPQILHGECVAIGMVKEAELARHLGILKGVAVSRIVKCLAAYGLPTSLKDARIRKLTAGKHCSVDQLMFNMALDKKNDGPKKKIVLLSAIGTPYETRASVVANEDIRVVLAP 393
               SCOP domains d1nvdb_ B: Dehydroquinate synthase, DHQS                                                                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains 1nvdB01 B:4-182  [code=3.40.50.1970, no name defined]                                                                                                                              1nvdB02 B:183-391 Dehydroquinate synthas        e-like - alpha domain                                                                                                                                            -- CATH domains
           Pfam domains (1) ----------------------------------------------------------------------DHQ_synthase-1nvdB01 B:74-359                                                                                                                                                                                                                                                                 ---------------------------------- Pfam domains (1)
           Pfam domains (2) ----------------------------------------------------------------------DHQ_synthase-1nvdB02 B:74-359                                                                                                                                                                                                                                                                 ---------------------------------- Pfam domains (2)
         Sec.struct. author .eeeee..eeeeeee.hhhhhhhhhhhhhhh...eeeeeeehhhhhhhhhhhhhhhhhhhh......eeeeeee..hhhhhhhhhhhhhhhhhhhh........eeeeeehhhhhhhhhhhhhhhhhh.eeeeee.hhhhhhh.....eeeeee..eeeeeeee....eeeee.hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh--------.hhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.......hhhhhhhh.....hhhhhhhhhh..........ee..eee..ee.....ee.hhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1nvd B   4 PTKISILGRESIIADFGLWRNYVAKDLISDCSSTTYVLVTDTNIGSIYTPSFEEAFRKRAAEITPSPRLLIYNRPPGEVSKSRQTKADIEDWMLSQNPPCGRDTVVIALGGGVIGDLTGFVASTYMRGVRYVQVPTTLLAMVDSSIGGKTAIDTPLGKNLIGAIWQPTKIYIDLEFLETLPVREFINGMAEVIKTAAISSEEEFTALEENAETILKAVR--------RFEGTEEILKARILASARHKAYVVSADEREGGLRNLLNWGHSIGHAIEAILTPQILHGECVAIGMVKEAELARHLGILKGVAVSRIVKCLAAYGLPTSLKDARIRKLTAGKHCSVDQLMFNMALDKKNDGPKKKIVLLSAIGTPYETRASVVANEDIRVVLAP 393
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213        |-       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393
                                                                                                                                                                                                                                                    222      231                                                                                                                                                                  

   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  (1, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: DHQS (27)

(-) Gene Ontology  (21, 21)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (ARO1_EMENI | P07547)
molecular function
    GO:0003855    3-dehydroquinate dehydratase activity    Catalysis of the reaction: 3-dehydroquinate = 3-dehydroshikimate + H(2)O.
    GO:0003856    3-dehydroquinate synthase activity    Catalysis of the reaction: 7-phospho-2-dehydro-3-deoxy-D-arabino-heptonate = 3-dehydroquinate + phosphate.
    GO:0003866    3-phosphoshikimate 1-carboxyvinyltransferase activity    Catalysis of the reaction: 3-phosphoshikimate + phosphoenolpyruvate = 5-O-(1-carboxyvinyl)-3-phosphoshikimate + phosphate.
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    GO:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    GO:0004764    shikimate 3-dehydrogenase (NADP+) activity    Catalysis of the reaction: shikimate + NADP+ = 3-dehydroshikimate + NADPH + H+.
    GO:0004765    shikimate kinase activity    Catalysis of the reaction: ATP + shikimate = 3-phosphoshikimate + ADP + 2 H(+).
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
    GO:0016765    transferase activity, transferring alkyl or aryl (other than methyl) groups    Catalysis of the transfer of an alkyl or aryl (but not methyl) group from one compound (donor) to another (acceptor).
biological process
    GO:0009073    aromatic amino acid family biosynthetic process    The chemical reactions and pathways resulting in the formation of aromatic amino acid family, amino acids with aromatic ring (phenylalanine, tyrosine, tryptophan).
    GO:0008652    cellular amino acid biosynthetic process    The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents.
    GO:0009423    chorismate biosynthetic process    The chemical reactions and pathways resulting in the formation of the unsymmetrical ether derived from phosphoenolpyruvate and 5-phosphoshikimic acid formed as an intermediate in the biosynthesis of aromatic amino acids and many other compounds.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
    GO:0016310    phosphorylation    The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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 Related Entries

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

UniProtKB/Swiss-Prot
        ARO1_EMENI | P075471dqs 1nr5 1nrx 1nua 1nva 1nvb 1nve 1nvf 1sg6

(-) Related Entries Specified in the PDB File

1nr5 CRYSTAL STRUCTURE OF 3-DEHYDROQUINATE SYNTHASE (DHQS) IN COMPLEX WITH ZN2+, NAD AND CARBAPHOSPHONATE, CRYSTAL FORM C, CLOSED FORM WITH COFACTOR
1nrx CRYSTAL STRUCTURE OF 3-DEHYDROQUINATE SYNTHASE (DHQS) IN COMPLEX WITH ZN2+ AND NAD, CRYSTAL FORM F, OPEN FORM WITH COFACTOR
1nua CRYSTAL STRUCTURE OF 3-DEHYDROQUINATE SYNTHASE (DHQS) IN COMPLEX WITH ZN2+, APO, CRYSTAL FORM D, OPEN FORM
1nva CRYSTAL STRUCTURE OF 3-DEHYDROQUINATE SYNTHASE (DHQS) IN COMPLEX WITH ZN2+ AND ADP, CRYSTAL FORM D, OPEN FORM WITH CO-FACTOR ANALOGUE
1nvb CRYSTAL STRUCTURE OF 3-DEHYDROQUINATE SYNTHASE (DHQS) IN COMPLEX WITH ZN2+ AND CARBAPHOSPHONATE, CRYSTAL FORM C, CLOSED FORM WITH SUBSTRATE ANALOGUE AND REDUCED CO-FACTOR
1nve CRYSTAL STRUCTURE OF 3-DEHYDROQUINATE SYNTHASE (DHQS) IN COMPLEX WITH ZN2+ AND NAD, CRYSTAL FORM E, OPEN FORM WITH COFACTOR
1nvf CRYSTAL STRUCTURE OF 3-DEHYDROQUINATE SYNTHASE (DHQS) IN COMPLEX WITH ZN2+, ADP AND CARBAPHOSPHONATE, CRYSTAL FORM H, CLOSED FORM WITH CO-FACTOR ANALOGUE AND SUBSTRATE ANALOGUE