Structure of PDB 2ybe Chain A

Receptor sequence
>2ybeA (length=410) Species: 9606 (Homo sapiens) [Search protein sequence]
LSNKLTLDKLDVKGKRVVMRVDFNVPMKNNQITNNQRIKAAVPSIKFCLD
NGAKSVVLMSHLGRPDGVPMPDKYSLEPVAVELKSLLGKDVLFLKDCVGP
EVEKACANPAAGSVILLENLRFHVEEEGKGKKVKAEPAKIEAFRASLSKL
GDVYVNDAFGTAHRAHSSMVGVNLPQKAGGFLMKKELNYFAKALESPERP
FLAILGGAKVADKIQLINNMLDKVNEMIIGGGMAFTFLKVLNNMEIGTSL
FDEEGAKIVKDLMSKAEKNGVKITLPVDFVTADKFDENAKTGQATVASGI
PAGWMGLDCGPESSKKYAEAVTRAKQIVWNGPVGVFEWEAFARGTKALMD
EVVKATSRGCITIIGGGDTATCCAKWNTEDKVSHVSTGGGASLELLEGKV
LPGVDALSNI
3D structure
PDB2ybe Interaction of Human 3-Phosphoglycerate Kinase with its Two Substrates: Is Substrate Antagonism a Kinetic Advantage?
ChainA
Resolution2.0 Å
3D
structure
Catalytic site residues are labeled in the structure
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Enzymatic activity
Catalytic site (original residue number in PDB) R38 K215 G373 G396
Catalytic site (residue number reindexed from 1) R37 K209 G367 G390
Enzyme Commision number 2.7.2.3: phosphoglycerate kinase.
Interaction with ligand
Site
#		 Ligand Ligand
chain		 Binding residues on receptor
(original residue number in PDB)		 Binding residues on receptor
(residue number reindexed from 1)		 Binding affinity
BS01 LA8 A G213 A214 K215 K219 L256 F291 N336 P338 G340 V341 F342 E343 G372 D374 T375 G207 A208 K209 K213 L250 F285 N330 P332 G334 V335 F336 E337 G366 D368 T369
BS02 ALF A R38 K215 K219 G372 G395 R37 K209 K213 G366 G389
Gene Ontology
Molecular Function
GO:0004618 phosphoglycerate kinase activity
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0016301 kinase activity
GO:0043531 ADP binding
GO:0047134 protein-disulfide reductase (NAD(P)H) activity
Biological Process
GO:0006094 gluconeogenesis
GO:0006096 glycolytic process
GO:0016310 phosphorylation
GO:0016525 negative regulation of angiogenesis
GO:0030855 epithelial cell differentiation
GO:0031639 plasminogen activation
GO:0061621 canonical glycolysis
GO:0071456 cellular response to hypoxia
Cellular Component
GO:0005615 extracellular space
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0016020 membrane
GO:0045121 membrane raft
GO:0070062 extracellular exosome

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:2ybe, PDBe:2ybe, PDBj:2ybe
PDBsum2ybe
PubMed21549713
UniProtP00558|PGK1_HUMAN Phosphoglycerate kinase 1 (Gene Name=PGK1)

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