Structure of PDB 2qf7 Chain B Binding Site BS04

Receptor Information

>2qf7 Chain B (length=1017) Species: 347834 (Rhizobium etli CFN 42)

GPISKILVANRSEIAIRVFRAANELGIKTVAIWAEEDKLALHRFKADESY
QVGRGPHLRDLGPIESYLSIDEVIRVAKLSGADAIHPGYGLLSESPEFVD
ACNKAGIIFIGPKADTMRQLGNKVAARNLAISVGVPVVPATEPLPPVMLK
ASMRVIRVYLEKLVERARHVESQILGDTHGNVVHLFERDCSVQRRNQKVV
ERAPAPYLSEAQRQELAAYSLKIAGATNYIGAGTVEYLMDADTGKFYFIE
VNPRIQVEHTVTEVVTGIDIVKAQIHILDGAAIGTPQSGVPNQEDIRLNG
HALQCRVTTEDPEHNFIPDYGRITAYRSASGFGIRLDGGTSYSGAIITRY
YDPLLVKVTAWAPNPLEAISRMDRALREFRIRGVATNLTFLEAIIGHPKF
RDNSYTTRFIDTTPELFQQVRQDRATKLLTYLADVTVNGHPEAKDRPKPL
EAARPVVPYGNGVKDGTKQLLDTLGPKKFGEWMRNEKRVLLTDTTMRDGH
QSLLATRMRTYDIARIAGTYSHALPNLLSLECWGGATFDVSMRFLTEDPW
ERLALIREGAPNLLLQMLLRGANGVGYTNYPDNVVKYFVRQAAKGGIDLF
RVFDCLNWVENMRVSMDAIAEENKLCEAAICYTGDILNSARPKYDLKYYT
NLAVELEKAGAHIIAVKDMAGLLKPAAAKVLFKALREATGLPIHFHTHDT
SGIAAATVLAAVEAGVDAVDAAMDALSGNTSQPCLGSIVEALSGSERDPG
LDPAWIRRISFYWEAVRNQYAAFESDLKGPASEVYLHEMPGGQFTNLKEQ
ARSLGLETRWHQVAQAYADANQMFGDIVKVTPSSKVVGDMALMMVSQDLT
VADVVSPDREVSFPESVVSMLKGDLGQPPSGWPEALQKKALKGEKPYTVR
PGSLLKEADLDAERKVIEKKLEREVSDFEFASYLMYPKVFTDFALASDTY
GPVSVLPTPAYFYGLADGEELFADIEKGKTLVIVNQAVSATDSQGMVTVF
FELNGQPRRIKVPDRAH

Ligand information

• Ligand ID: AGS
• InChI: InChI=1S/C10H16N5O12P3S/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(25-10)1-24-28(18,19)26-29(20,21)27-30(22,23)31/h2-4,6-7,10,16-17H,1H2,(H,18,19)(H,20,21)(H2,11,12,13)(H2,22,23,31)/t4-,6-,7-,10-/m1/s1
• InChIKey: NLTUCYMLOPLUHL-KQYNXXCUSA-N
• SMILES:
  OpenEye OEToolkits 1.7.6: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=S)(O)O)O)O)N
  CACTVS 3.370: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=S)[C@@H](O)[C@H]3O
  CACTVS 3.370: Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=S)[CH](O)[CH]3O
  OpenEye OEToolkits 1.7.6: c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)OP(=O)(O)OP(=S)(O)O)O)O)N
  ACDLabs 12.01: O=P(O)(OP(=S)(O)O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
• Formula: C10 H16 N5 O12 P3 S
• Name: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER;
  ATP-GAMMA-S;
  ADENOSINE 5'-(3-THIOTRIPHOSPHATE);
  ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE);
  ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE
• ChEMBL: CHEMBL131890
• DrugBank: DB02930
• ZINC: ZINC000008295128
• PDB chain: 2qf7 Chain B Residue 1161

Receptor-Ligand Complex Structure

Structure summary

• PDB: 2qf7 Domain architecture of pyruvate carboxylase, a biotin-dependent multifunctional enzyme
• Resolution: 2.0 Å
• Binding residue (original residue number in PDB): M164 K166 M176 E208 V211 H216 Q240 E283 L285 I296 E297 T454
• Binding residue (residue number reindexed from 1): M148 K150 M153 E161 V164 H169 Q193 E236 L238 I249 E250 T407
• Annotation score: 4

Enzymatic activity

• Catalytic site (original residue number in PDB): K124 K166 H216 R242 T281 E283 E297 N299 R301 E305 R353 D549 D655 K718 H747 H749 T882
• Catalytic site (residue number reindexed from 1): K123 K150 H169 R195 T234 E236 E250 N252 R254 E258 R306 D498 D604 K667 H696 H698 T831
• 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:0046872 metal ion binding

Biological Process

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

Cellular Component

• GO:0005737 cytoplasm

External links

• PDB: RCSB:2qf7, PDBe:2qf7, PDBj:2qf7
• PDBsum: 2qf7
• PubMed: 17717183
• UniProt: Q2K340