Structure of PDB 13pk Chain C Binding Site BS01

Receptor Information
>13pk Chain C (length=415) Species: 5691 (Trypanosoma brucei) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EKKSINECDLKGKKVLIRVDFNVPVKNGKITNDYRIRSALPTLKKVLTEG
GSCVLMSHLGRPKGIPMAQAGKIRSTGGVPGFQQKATLKPVAKRLSELLL
RPVTFAPDCLNAADVVSKMSPGDVVLLENVRFYKEEGSKKAKDREAMAKI
LASYGDVYISDAFGTAHRDSATMTGIPKILGNGAAGYLMEKEISYFAKVL
GNPPRPLVAIVGGAKVSDKIQLLDNMLQRIDYLLIGGAMAYTFLKAQGYS
IGKSKCEESKLEFARSLLKKAEDRKVQVILPIDHVCHTEFKAVDSPLITE
DQNIPEGHMALDIGPKTIEKYVQTIGKCKSAIWNGPMGVFEMVPYSKGTF
AIAKAMGRGTHEHGLMSIIGGGDSASAAELSGEAKRMSHVSTGGGASLEL
LEGKTLPGVTVLDDK
Ligand information
Ligand IDADP
InChIInChI=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
InChIKeyXTWYTFMLZFPYCI-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(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 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N
FormulaC10 H15 N5 O10 P2
NameADENOSINE-5'-DIPHOSPHATE
ChEMBLCHEMBL14830
DrugBankDB16833
ZINCZINC000012360703
PDB chain13pk Chain C Residue 421 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB13pk Synergistic effects of substrate-induced conformational changes in phosphoglycerate kinase activation.
Resolution2.5 Å
Binding residue
(original residue number in PDB)		G217 A218 K219 Y245 P340 G342 V343 E345 G375 D377 S378
Binding residue
(residue number reindexed from 1)		G213 A214 K215 Y241 P336 G338 V339 E341 G371 D373 S374
Annotation score5
Enzymatic activity
Catalytic site (original residue number in PDB) R39 K219 G376 G399
Catalytic site (residue number reindexed from 1) R35 K215 G372 G395
Enzyme Commision number 2.7.2.3: phosphoglycerate kinase.
Gene Ontology
Molecular Function
GO:0004618 phosphoglycerate kinase activity
GO:0005524 ATP binding
GO:0016301 kinase activity
GO:0043531 ADP binding
Biological Process
GO:0006094 gluconeogenesis
GO:0006096 glycolytic process
GO:0016310 phosphorylation
Cellular Component
GO:0005829 cytosol
GO:0020015 glycosome

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:13pk, PDBe:13pk, PDBj:13pk
PDBsum13pk
PubMed9000079
UniProtP07378|PGKC_TRYBB Phosphoglycerate kinase, glycosomal

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