Structure of PDB 3hb9 Chain A Binding Site BS01

Receptor Information

>3hb9 Chain A (length=1133) Species: 158878 (Staphylococcus aureus subsp. aureus Mu50)

QIKKLLVANRGEIAIRIFRAAAELDISTVAIYSNEDKSSLHRYKADESYL
VGSDLGPAESYLNIERIIDVAKQANVDAIHPGYGFLSENEQFARRCAEEG
IKFIGPHLEHLDMFGDKVKARTTAIKADLPVIPGTDGPIKSYELAKEFAE
EAGFPLMIKATSRIVREESELEDAFHRAKSEAEKSEVYIERYIDNPKHIE
VQVIGDEHGNIVHLFERDCSVQRRHQKVVEVAPSVGLSPTLRQRICDAAI
QLMENIKYVNAGTVEFLVSGDEFFFIEVNPRVQVEHTITEMVTGIDIVKT
QILVAAGADLFGEEINMPQQKDITTLGYAIQCRITTEDPLNDFMPDTGTI
IAYRSSGGFGVRLDAGDGFQGAEISPYYDSLLVKLSTHAISFKQAEEKMV
RSLREMRIRGVKTNIPFLINVMKNKKFTSGDYTTKFIEETPELFDIQPSL
DRGTKTLEYIGNVTINGFPNVEKRPKPDYELASIPTVSSSKIASFSGTKQ
LLDEVGPKGVAEWVKKQDDVLLTDTTFRDAHQSLLATRVRTKDMINIASK
TADVFKDGFSLEMWGGTTFDVAYNFLKENPWERLERLRKAIPNVLFQMLL
RASNAVGYKNYPDNVIHKFVQESAKAGIDVFRIFDSLNWVDQMKVANEAV
QEAGKISEGTICYTGDILNPERSNIYTLEYYVKLAKELEREGFHILAIKD
MAGLLKPKAAYELIGELKSAVDLPIHLHTHDTSGNGLLTYKQAIDAGVDI
IDTAVASMSGLTSQPSANSLYYALNGFPRHLRTDIEGMESLSHYWSTVRT
YYSDFESDIKSPNTEIYQHEMPGGQYSNLSQQAKSLGLGERFDEVKDMYR
RVNFLFGDIVKVTPSSKVVGDMALYMVQNDLDEQSVITDGYKLDFPESVV
SFFKGEIGQPVNGFNKDLQAVILKGQEALTARPGEYLEPVDFEKVRELLE
EEQQGPVTEQDIISYVLYPKVYEQYIQTRNQYGNLSLLDTPTFFFGMRNG
ETVEIEIDKGKRLIIKLETISEPDENGNRTIYYAMNGQARRIYIKDENVH
TNANVKPKADKSNPSHIGAQMPGSVTEVKVSVGETVKANQPLLITEAMKM
ETTIQAPFDGVIKQVTVNNGDTIATGDLLIEIE

Ligand information

• Ligand ID: ADP
• InChI: InChI=1S/C10H15N5O10P2/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(24-10)1-23-27(21,22)25-26(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
• InChIKey: XTWYTFMLZFPYCI-KQYNXXCUSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O)O)N
  CACTVS 3.341: Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
  ACDLabs 10.04: O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
  CACTVS 3.341: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
  OpenEye OEToolkits 1.5.0: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N
• Formula: C10 H15 N5 O10 P2
• Name: ADENOSINE-5'-DIPHOSPHATE
• ChEMBL: CHEMBL14830
• DrugBank: DB16833
• ZINC: ZINC000012360703
• PDB chain: 3hb9 Chain A Residue 2100

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3hb9 A Symmetrical Tetramer for S. aureus Pyruvate Carboxylase in Complex with Coenzyme A.
• Resolution: 2.9 Å
• Binding residue (original residue number in PDB): K152 M192 Y238 I239 H244 Q268 H271 L313 I323 E324
• Binding residue (residue number reindexed from 1): K117 M157 Y192 I193 H198 Q222 H225 L267 I276 E277
• Annotation score: 5

Enzymatic activity

• Catalytic site (original residue number in PDB): K152 K194 H244 R270 T309 E311 E324 N326 R328 E332 R377 D572 D678 K741 H771 H773 I794 S800 M801 T840 T908 S910 V922 N924 Q929
• Catalytic site (residue number reindexed from 1): K117 K159 H198 R224 T263 E265 E277 N279 R281 E285 R333 D529 D635 K699 H728 H730 I751 S757 M758 T797 T863 S865 V877 N879 Q884
• Enzyme Commision number: 6.4.1.1: pyruvate carboxylase.

Gene Ontology

Molecular Function

• GO:0003824 catalytic activity
• GO:0004736 pyruvate carboxylase activity
• GO:0005524 ATP binding
• GO:0016874 ligase activity
• GO:0042802 identical protein binding
• GO:0046872 metal ion binding

Biological Process

• GO:0006090 pyruvate metabolic process
• GO:0006094 gluconeogenesis

Cellular Component

• GO:0005737 cytoplasm

External links

• PDB: RCSB:3hb9, PDBe:3hb9, PDBj:3hb9
• PDBsum: 3hb9
• PubMed: 19523900
• UniProt: A0A0H3JRU9|PYC_STAAM Pyruvate carboxylase (Gene Name=pycA)