Structure of PDB 3bg5 Chain A Binding Site BS04

Receptor Information

>3bg5 Chain A (length=1137) Species: 1280 (Staphylococcus aureus)

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

Ligand information

• Ligand ID: BTI
• InChI: InChI=1S/C10H16N2O2S/c13-5-3-1-2-4-8-9-7(6-15-8)11-10(14)12-9/h5,7-9H,1-4,6H2,(H2,11,12,14)/t7-,8-,9-/m0/s1
• InChIKey: ARDNWGMSCXSPBF-CIUDSAMLSA-N
• SMILES:
  CACTVS 3.341: O=CCCCC[CH]1SC[CH]2NC(=O)N[CH]12
  CACTVS 3.341: O=CCCCC[C@@H]1SC[C@@H]2NC(=O)N[C@H]12
  OpenEye OEToolkits 1.5.0: C1[C@H]2[C@@H]([C@@H](S1)CCCCC=O)NC(=O)N2
  ACDLabs 10.04: O=C1NC2C(SCC2N1)CCCCC=O
  OpenEye OEToolkits 1.5.0: C1C2C(C(S1)CCCCC=O)NC(=O)N2
• Formula: C10 H16 N2 O2 S
• Name: 5-(HEXAHYDRO-2-OXO-1H-THIENO[3,4-D]IMIDAZOL-6-YL)PENTANAL
• DrugBank: DB07497
• ZINC: ZINC000036470912
• PDB chain: 3bg5 Chain B Residue 2000

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3bg5 Crystal structures of human and Staphylococcus aureus pyruvate carboxylase and molecular insights into the carboxyltransfer reaction.
• Resolution: 2.8 Å
• Binding residue (original residue number in PDB): Y503 G511 F512 P513 F618
• Binding residue (residue number reindexed from 1): Y463 G471 F472 P473 F579
• Annotation score: 1

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:3bg5, PDBe:3bg5, PDBj:3bg5
• PDBsum: 3bg5
• PubMed: 18297087
• UniProt: A0A0H3JRU9|PYC_STAAM Pyruvate carboxylase (Gene Name=pycA)