Structure of PDB 4hnt Chain A Binding Site BS01

Receptor Information

>4hnt Chain A (length=1052) Species: 1280 (Staphylococcus aureus)

QIKKLLVANRGEIAIRIFRAAAELDISTVAIYSNEDKSSLHRYKADESYL
VGSDLGPAESYLNIERIIDVAKQANVDAIHPGYGFLSENEQFARRCAEEG
IKFIGPHLEHLDMFGDKVKARTTAIKADLPVIPGTDGPIKSYELAKEFAE
EAGFPLMIKATSRIVREESELEDAFHRAKSEAEKSFGNSEVYIERYIDNP
KHIEVQVIGDEHGNIVHLFERDCSVQRRHQKVVEVAPSVGLSPTLRQRIC
DAAIQLMENIKYVNAGTVEFLVSGDEFFFIEVNPRVQVEHTITEMVTGID
IVKTQILVAAGADLFGEEINMPQQKDITTLGYAIQCRITTEDPLNDFMPD
TGTIIAYRSSGGAGVRLDAGDGFQGAEISPYYDSLLVKLSTHAISFKQAE
EKMVRSLREMRIRGVKTNIPFLINVMKNKKFTSGDYTTKFIEETPELFDI
QPSLDRGTKTLEYIGNVTINGFPNVEKRPKPDYELASIPTVSSSKIASFS
GTKQLLDEVGPKGVAEWVKKQDDVLLTDTTFRDAHQSLLATRVRTKDMIN
IASKTADVFKDGFSLEMWGGATFDVAYNFLKENPWERLERLRKAIPNVLF
QMLLRASNAVGYKNYPDNVIHKFVQESAKAGIDVFRIFDSLNWVDQMKVA
NEAVQEAGKISEGTICYTGDILNPERSNIYTLEYYVKLAKELEREGFHIL
AIKDMAGLLKPKAAYELIGELKSAVDLPIHLHTHDTSGNGLLTYKQAIDA
GVDIIDTAVASMSGLTSQPSANSLYYALNGFPRHLRTDIEGMESLSHYWS
TVRTYYSDFESDIKSPNTEIYQHEMPGGQYSNLSQQAKSLGLGERFDEVK
DMYRRVNFLFGDIVKVTPSSKVVGDMALYMVQNDLDEQSVITDGYKLDFP
ESVVSFFKGEIGQPVNGFNKDLQAVILKGQEALTARPGEYLEPVDFEKVR
ELLEEEQQGPVTEQDIISYVLYPKVYEQYIQTRNQYGNLSLLDTPTFFFG
MRNGETVEIEIDKGKRLIIKLETISEPDENGNRTIYYAMNGQARRIYIKD
EN

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: 4hnt Chain A Residue 1201

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4hnt Characterizing the Importance of the Biotin Carboxylase Domain Dimer for Staphylococcus aureus Pyruvate Carboxylase Catalysis.
• Resolution: 2.8 Å
• Binding residue (original residue number in PDB): M192 K194 I239 H244 Q268 L313 I323 E324
• Binding residue (residue number reindexed from 1): M157 K159 I197 H202 Q226 L271 I280 E281
• Annotation score: 5

Enzymatic activity

• Catalytic site (original residue number in PDB): K152 K194 S231 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 S189 H202 R228 T267 E269 E281 N283 R285 E289 R337 D533 D639 K703 H732 H734 I755 S761 M762 T801 T867 S869 V881 N883 Q888
• 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:4hnt, PDBe:4hnt, PDBj:4hnt
• PDBsum: 4hnt
• PubMed: 23286247
• UniProt: A0A0H3JRU9|PYC_STAAM Pyruvate carboxylase (Gene Name=pycA)