Structure of PDB 4kcu Chain A Binding Site BS03

Receptor Information

>4kcu Chain A (length=498) Species: 5702 (Trypanosoma brucei brucei)

SQLEHNIGLSIFEPVAKHRANRIVCTIGPSTQSVEALKNLMKSGMSVARM
NFSHGSHEYHQTTINNVRAAAAELGLHIGIALDTKGPEIRTGLFKDGEVS
FAPGDIVCVTTDPAYEKVGTKEKFYIDYPQLTNAVRPGGSIYVDDGVMTL
RVVSKEDDRTLKCHVNNHHRLTDRRGINLPGCEVDLPAVSEKDRKDLEFG
VAQGVDMIFASFIRTAEQVREVRAALGEKGKDILIISKIENHQGVQNIDS
IIEASNGIMVARGDLGVEIPAEKVCVAQMCIISKCNVVGKPVICATQMLE
SMTSNPRPTRAEVSDVANAVLNGADCVMLSGETAKGKYPNEVVQYMARIC
VEAQSATHDTVMFNSIKNLQKIPMCPEEAVCSSAVASAFEVQAKAMLVLS
NTGRSARLISKYRPNCPIICVTTRLQTCRQLNVTRSVVSVFYDAAKSGED
KDKEKRVKLGLDFAKKEKYASTGDVVVVVHADHSVKGYPNQTRLIYLP

Ligand information

• Ligand ID: FDP
• InChI: InChI=1S/C6H14O12P2/c7-2-6(18-20(13,14)15)5(9)4(8)3(17-6)1-16-19(10,11)12/h3-5,7-9H,1-2H2,(H2,10,11,12)(H2,13,14,15)/t3-,4-,5+,6+/m1/s1
• InChIKey: YXWOAJXNVLXPMU-ZXXMMSQZSA-N
• SMILES:
  ACDLabs 10.04: O=P(OC1(OC(C(O)C1O)COP(=O)(O)O)CO)(O)O
  OpenEye OEToolkits 1.5.0: C([C@@H]1[C@H]([C@@H]([C@](O1)(CO)OP(=O)(O)O)O)O)OP(=O)(O)O
  CACTVS 3.341: OC[C]1(O[CH](CO[P](O)(O)=O)[CH](O)[CH]1O)O[P](O)(O)=O
  CACTVS 3.341: OC[C@]1(O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@@H]1O)O[P](O)(O)=O
  OpenEye OEToolkits 1.5.0: C(C1C(C(C(O1)(CO)OP(=O)(O)O)O)O)OP(=O)(O)O
• Formula: C6 H14 O12 P2
• Name: 2,6-di-O-phosphono-beta-D-fructofuranose;
  FRUCTOSE-2,6-DIPHOSPHATE;
  2,6-di-O-phosphono-beta-D-fructose;
  2,6-di-O-phosphono-D-fructose;
  2,6-di-O-phosphono-fructose
• ZINC: ZINC000004228295
• PDB chain: 4kcu Chain A Residue 1004

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4kcu Pyruvate kinases have an intrinsic and conserved decarboxylase activity.
• Resolution: 2.35 Å
• Binding residue (original residue number in PDB): L400 S401 N402 T403 S406 K454 R457 H481 A482 K487 G488 Y489
• Binding residue (residue number reindexed from 1): L399 S400 N401 T402 S405 K453 R456 H480 A481 K486 G487 Y488
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): R50 R91 K239 T297
• Catalytic site (residue number reindexed from 1): R49 R90 K238 T296
• Enzyme Commision number: 2.7.1.40: pyruvate kinase.

Gene Ontology

Molecular Function

• GO:0000287 magnesium ion binding
• GO:0003824 catalytic activity
• GO:0004743 pyruvate kinase activity
• GO:0005524 ATP binding
• GO:0016301 kinase activity
• GO:0030955 potassium ion binding
• GO:0046872 metal ion binding

Biological Process

• GO:0006096 glycolytic process
• GO:0016310 phosphorylation

Cellular Component

• GO:0005737 cytoplasm

External links

• PDB: RCSB:4kcu, PDBe:4kcu, PDBj:4kcu
• PDBsum: 4kcu
• PubMed: 24328825
• UniProt: P30615|KPYK1_TRYBB Pyruvate kinase 1 (Gene Name=PYK1)