Structure of PDB 6hqv Chain B Binding Site BS06

Receptor Information

>6hqv Chain B (length=1536) Species: 759272 (Thermochaetoides thermophila DSM 1495)

EPTRIAILGKEDIIVDHGIWLNFVAHDLLQTLPSSTYVLITDTNLYTTYV
PPFQAVFEAAAPRDVRLLTYAIPPGEYSKSRETKAEIEDWMLSHACTRDT
VIIALGGGVIGDMIGYVAATFMRGVRFVQVPTTLLAMVDSSIGGKTAIDT
PMGKNLIGAFWQPRRIYIDLAFLETLPVREFINGMAEVIKTAAIWNETEF
TALEENAAAILEAVRSKASSPAARLAPIRHILKRIVLGSARVKAEVVSAD
EREGGLRNLLNFGHSIGHAYEAILAPQVLHGECVAIGMVKEAELARYLGV
LRPSAVARLTKLIASYDLPTSVHDKRIAKLSAGKECPVDVLLQKMAVDKK
NEGRKKKIVLLSAIGKTYEKKATVVDDRAIRLVLSPSVRVTPGVPKGLSV
TVTPPGSKSISNRALVLAALGEGTTRIHGLLHSDDVQYMLAAIEQLHGAD
FSWEDAGEILVVTGKGGKLQASKEPLYLGNAGTASRFLTSVVALCAPSAV
SSTVLTGNARMKVRPIGALVDALRANGVGVKYLEKEKSLPVEVDAAGGFA
GGVIELAATVSSQYVSSILMAAPYAHQPVTLRLVGGKPISQPYIDMTIAM
MASFGIKVERSAEDPNTYLIPKGVYKNPPEYVVESDASSATYPLAVAAIT
GTTCTIPNIGSESLQGDARFAVEVLRPMGCAVEQTATSTTVTGPPIGTLK
AIPHVDMEPMTDAFLTAAVLAAVADGTTQITGIANQRVKECNRIAAMKDQ
LAKFGVQCNELEDGIEVIGKPYQELRNPVEGIYCYDDHRVAMSHSVLSTI
SPHPVLILERECTAKTWPGWWDILSQFFKVQLDGEEDPTGTDRSIFIVGM
RGAGKSTAGRWMSELLKRPLVDLDAELERREGMTIPEIIRGERGWEGFRQ
AELELLQDVIKNQSKGYIFSCGGGIVETEAARKLLIDYHKNGGPVLLVHR
DNIREVYERRKPWFYECSNLQYHSPHEDGSEALLQPPADFARFVKLIAGQ
STHLEDVRAKKHSFFVSLTVPNVADALDIIPRVVVGSDAVELRVDLLESY
EPEFVARQVALLRAAAQVPIVYTVRTQSQGGKFPDEDYDLALRLYQTGLR
SGVEYLDLEMTMPDHILQAVTDAKGFTSIIASHHDPQCKLSWKSGSWIPF
YNKALQYGDVIKLVGVAREMADNFALTNFKAKMLAAHDNKPMIALNMGTA
GKLSRVLNGFLTPVSHPALPSKAAPGQLSATEIRQALSLIGEIEPKSFYL
FGKPISASRSPALHNTLFYKTGLPHHYSRFETDEASKALESLIRSPDFGG
ASVTIPLKLDIMPLLDSATDAARTIGAVNTIIPQTRDGSTTTLVGDNTDW
RGMVHALLHSSGSGSVVQRTAAPRGAAMVVGSGGTARAAIYALHDLGFAP
IWIVARSEERVAELVRGFDGYDLRRMTSPHQGKDNMPSVVISTIPATQPI
DPSMREVIVEVLKHGHPSAEGKVLLEMAYQPPRTPLMTLAEDQGWRTVGG
LEVLAAQGWYQFQLWTGITPLYEEARAAVMGEDSVE

Ligand information

• Ligand ID: SKM
• InChI: InChI=1S/C7H10O5/c8-4-1-3(7(11)12)2-5(9)6(4)10/h1,4-6,8-10H,2H2,(H,11,12)/t4-,5-,6-/m1/s1
• InChIKey: JXOHGGNKMLTUBP-HSUXUTPPSA-N
• SMILES:
  CACTVS 3.341: O[C@@H]1CC(=C[C@@H](O)[C@H]1O)C(O)=O
  OpenEye OEToolkits 1.5.0: C1C(C(C(C=C1C(=O)O)O)O)O
  OpenEye OEToolkits 1.5.0: C1[C@H]([C@@H]([C@@H](C=C1C(=O)O)O)O)O
  CACTVS 3.341: O[CH]1CC(=C[CH](O)[CH]1O)C(O)=O
  ACDLabs 10.04: O=C(O)C1=CC(O)C(O)C(O)C1
• Formula: C7 H10 O5
• Name: (3R,4S,5R)-3,4,5-TRIHYDROXYCYCLOHEX-1-ENE-1-CARBOXYLIC ACID;
  SHIKIMATE
• ChEMBL: CHEMBL290345
• ZINC: ZINC000003860720
• PDB chain: 6hqv Chain B Residue 1607

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6hqv Architecture and functional dynamics of the pentafunctional AROM complex.
• Resolution: 3.0 Å
• Binding residue (original residue number in PDB): D900 G949 G950 R1005
• Binding residue (residue number reindexed from 1): D874 G923 G924 R960
• Annotation score: 5

Enzymatic activity

• Catalytic site (original residue number in PDB): R137 K159 E201 K257 E267 R271 N275 H278 H282 H294
• Catalytic site (residue number reindexed from 1): R123 K145 E187 K243 E253 R257 N261 H264 H268 H280
• Enzyme Commision number: 1.1.1.25: shikimate dehydrogenase (NADP(+)).
  2.5.1.19: 3-phosphoshikimate 1-carboxyvinyltransferase.
  2.7.1.71: shikimate kinase.
  4.2.1.10: 3-dehydroquinate dehydratase.
  4.2.3.4: 3-dehydroquinate synthase.

Gene Ontology

Molecular Function

• GO:0003824 catalytic activity
• GO:0003855 3-dehydroquinate dehydratase activity
• GO:0003856 3-dehydroquinate synthase activity
• GO:0003866 3-phosphoshikimate 1-carboxyvinyltransferase activity
• GO:0004764 shikimate 3-dehydrogenase (NADP+) activity
• GO:0004765 shikimate kinase activity
• GO:0005524 ATP binding
• GO:0016301 kinase activity
• GO:0016491 oxidoreductase activity
• GO:0016765 transferase activity, transferring alkyl or aryl (other than methyl) groups
• GO:0016829 lyase activity
• GO:0046872 metal ion binding

Biological Process

• GO:0008652 amino acid biosynthetic process
• GO:0009073 aromatic amino acid family biosynthetic process
• GO:0009423 chorismate biosynthetic process
• GO:0016310 phosphorylation

Cellular Component

• GO:0005737 cytoplasm

External links

• PDB: RCSB:6hqv, PDBe:6hqv, PDBj:6hqv
• PDBsum: 6hqv
• PubMed: 32632294
• UniProt: G0S061