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Structure of PDB 1vjd Chain A Binding Site BS01

Receptor Information

>1vjd Chain A (length=416) Species: 9823 (Sus scrofa)

SLSNKLTLDKLDVKGKRVVMRVDFNVPMKNNQITNNQRIKAAIPSIKFCL
DNGAKSVVLMSHLGRPDGIPMPDKYSLEPVAVELKSLLGKDVLFLKDCVG
PEVEKACADPAAGSVILLENLRFHVEEEGKGKDASGSKVKADPAKIEAFR
ASLSKLGDVYVNDAFGTAHRAHSSMVGVNLPKKAGGFLMKKELNYFAKAL
ESPERPFLAILGGAKVADKIQLINNMLDKVNEMIIGGGMAFTFLKVLNNM
EIGTSLFDEEGSKIVKDLMSKAEKNGVKITLPVDFVTADKFDENAKTGQA
TVASGIPAGWMGLDCGPESSKKYSEAVARAKQIVWNGPVGVFEWEAFAQG
TKALMDEVVKATSRGCITIIGGGDTATCCAKWNTEDKVSHVSTGGGASLE
LLEGKVLPGVDALSNV

Ligand information

• Ligand ID: ATP
• InChI: InChI=1S/C10H16N5O13P3/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(26-10)1-25-30(21,22)28-31(23,24)27-29(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H,23,24)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
• InChIKey: ZKHQWZAMYRWXGA-KQYNXXCUSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O)N
  CACTVS 3.341: Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
  ACDLabs 10.04: O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
  OpenEye OEToolkits 1.5.0: c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=O)(O)O[P@](=O)(O)OP(=O)(O)O)O)O)N
  CACTVS 3.341: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@](O)(=O)O[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
• Formula: C10 H16 N5 O13 P3
• Name: ADENOSINE-5'-TRIPHOSPHATE
• ChEMBL: CHEMBL14249
• DrugBank: DB00171
• ZINC: ZINC000004261765
• PDB chain: 1vjd Chain A Residue 417

Receptor-Ligand Complex Structure

Structure summary

• PDB: 1vjd Role of phosphate chain mobility of MgATP in completing the 3-phosphoglycerate kinase catalytic site: binding, kinetic, and crystallographic studies with ATP and MgATP.
• Resolution: 1.9 Å
• Binding residue (original residue number in PDB): G213 A214 K219 G237 G238 G312 G337 P338 G340 V341 E343 G372 G373 D374 T375
• Binding residue (residue number reindexed from 1): G213 A214 K219 G237 G238 G312 G337 P338 G340 V341 E343 G372 G373 D374 T375
• Annotation score: 5
• Binding affinity: MOAD: Kd=0.286mM
  PDBbind-CN: -logKd/Ki=3.54,Kd=0.286mM

Enzymatic activity

• Catalytic site (original residue number in PDB): R38 K215 G373 G396
• Catalytic site (residue number reindexed from 1): R38 K215 G373 G396
• 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:0005737 cytoplasm
• GO:0005829 cytosol

External links

• PDB: RCSB:1vjd, PDBe:1vjd, PDBj:1vjd
• PDBsum: 1vjd
• PubMed: 15035615
• UniProt: Q7SIB7|PGK1_PIG Phosphoglycerate kinase 1 (Gene Name=PGK1)

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