Structure of PDB 3bg5 Chain D Binding Site BS03

Receptor Information

>3bg5 Chain D (length=1067) Species: 1280 (Staphylococcus aureus)

QIKKLLVANRGEIAIRIFRAAAELDISTVAIYSNEDKSSLHRYKADESYL
VGSDLGPAESYLNIERIIDVAKQANVDAIHPGYGFLSENEQFARRCAEEG
IKFIGPHLEHLDMFGDKVKARTTAIKADLPVIPIDNPKHIEVQVIGDEHG
NIVHLFERDCSVQRRHQKVVEVAPSVGLSPTLRQRICDAAIQLMENIKYV
NAGTVEFLVSGDEFFFIEVNPRVQVEHTITEMVTGIDIVKTQILVAAGAD
LFGEEINMPQQKDITTLGYAIQCRITTEDPLNDFMPDTGTIIAYRSSGGF
GVRLDAGDGFQGAEISPYYDSLLVKLSTHAISFKQAEEKMVRSLREMRIR
GVKTNIPFLINVMKNKKFTSGDYTTKFIEETPELFDIQPSLDRGTKTLEY
IGNVTINGFPNVEKRPKPDYELASIPTVSSSKIASFSGTKQLLDEVGPKG
VAEWVKKQDDVLLTDTTFRDAHQSLLATRVRTKDMINIASKTADVFKDGF
SLEMWGGATFDVAYNFLKENPWERLERLRKAIPNVLFQMLLRASNAVGYK
NYPDNVIHKFVQESAKAGIDVFRIFDSLNWVDQMKVANEAVQEAGKISEG
TICYTGDILNPERSNIYTLEYYVKLAKELEREGFHILAIKDMAGLLKPKA
AYELIGELKSAVDLPIHLHTHDTSGNGLLTYKQAIDAGVDIIDTAVASMS
GLTSQPSANSLYYALNGFPRHLRTDIEGMESLSHYWSTVRTYYSDFESDI
KSPNTEIYQHEMPGGQYSNLSQQAKSLGLGERFDEVKDMYRRVNFLFGDI
VKVTPSSKVVGDMALYMVQNDLDEQSVITDGYKLDFPESVVSFFKGEIGQ
PVNGFNKDLQAVILKGQEALTARPGEYLEPVDFEKVRELLEEEQQGPVTE
QDIISYVLYPKVYEQYIQTRNQYGNLSLLDTPTFFFGMRNGETVEIEIDK
GKRLIIKLETISEPDENGNRTIYYAMNGQARRIYIKDENKPKADKSNPSH
IGAQMPGSVTEVKVSVGETVKANQPLLITEAMKMETTIQAPFDGVIKQVT
VNNGDTIATGDLLIEIE

Ligand information

• Ligand ID: PYR
• InChI: InChI=1S/C3H4O3/c1-2(4)3(5)6/h1H3,(H,5,6)
• InChIKey: LCTONWCANYUPML-UHFFFAOYSA-N
• SMILES:
  CACTVS 3.385: CC(=O)C(O)=O
  OpenEye OEToolkits 1.7.6: CC(=O)C(=O)O
  ACDLabs 12.01: O=C(C(=O)O)C
• Formula: C3 H4 O3
• Name: PYRUVIC ACID
• ChEMBL: CHEMBL1162144
• DrugBank: DB00119
• ZINC: ZINC000001532517
• PDB chain: 3bg5 Chain D Residue 2001

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): L642 K741
• Binding residue (residue number reindexed from 1): L540 K640
• Annotation score: 5

Enzymatic activity

• Catalytic site (original residue number in PDB): K152 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 H139 R165 T204 E206 E218 N220 R222 E226 R274 D470 D576 K640 H669 H671 I692 S698 M699 T738 T804 S806 V818 N820 Q825
• 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)