Structure of PDB 2vgf Chain D Binding Site BS01

Receptor Information

>2vgf Chain D (length=512) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

QQQQLPAAMADTFLEHLCLLDIDSEPVAARSTSIIATIGPASRSVERLKE
MIKAGMNIARLNFSHGSHEYHAESIANVREAVESFAGSPLSYRPVAIALD
TKGPEIRTGPESEVELVKGSQVLVTVDPAFRTRGNANTVWVDYPNIVRVV
PVGGRIYIDDGLISLVVQKIGPEGLVTQVENGGVLGSRKGVNLPGAQVDL
PGLSEQDVRDLRFGVEHGVDIVFASFVRKASDVAAVRAALGPEGHGIKII
SKIENHEGVKRFDEILEVSDGIMVARGDLGIEIPAEKVFLAQKMMIGRCN
LAGKPVVCATQMLESMITKPRPMRAETSDVANAVLDGADCIMLSGETAKG
NFPVEAVKMQHAIAREAEAAVYHRQLFEELRRAAPLSRDPTEVTAIGAVE
AAFKCCAAAIIVLTTTGRSAQLLSRYRPRAAVIAVTRSAQAARQVHLCRG
VFPLLYREPPEAIWADDVDRRVQFGIESGKLRGFLRVGDLVIVVTGWRPG
SGYTNIMRVLSI

Ligand information

Ligand ID

FBP

InChI

InChI=1S/C6H14O12P2/c7-4-3(1-16-19(10,11)12)18-6(9,5(4)8)2-17-20(13,14)15/h3-5,7-9H,1-2H2,(H2,10,11,12)(H2,13,14,15)/t3-,4-,5+,6-/m1/s1

InChIKey

RNBGYGVWRKECFJ-ARQDHWQXSA-N

SMILES

Software	SMILES
CACTVS 3.341	O[C@H]1[C@H](O)[C@@](O)(CO[P](O)(O)=O)O[C@@H]1CO[P](O)(O)=O
CACTVS 3.341	O[CH]1[CH](O)[C](O)(CO[P](O)(O)=O)O[CH]1CO[P](O)(O)=O
ACDLabs 10.04	O=P(O)(O)OCC1OC(O)(COP(=O)(O)O)C(O)C1O
OpenEye OEToolkits 1.5.0	C(C1C(C(C(O1)(COP(=O)(O)O)O)O)O)OP(=O)(O)O
OpenEye OEToolkits 1.5.0	C([C@@H]1[C@H]([C@@H]([C@](O1)(COP(=O)(O)O)O)O)O)OP(=O)(O)O

Formula

C6 H14 O12 P2

Name

1,6-di-O-phosphono-beta-D-fructofuranose;
BETA-FRUCTOSE-1,6-DIPHOSPHATE;
FRUCTOSE-1,6-BISPHOSPHATE;
1,6-di-O-phosphono-beta-D-fructose;
1,6-di-O-phosphono-D-fructose;
1,6-di-O-phosphono-fructose

PDB chain

2vgf Chain D Residue 580 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]

Receptor-Ligand Complex Structure

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Structure summary

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PDB	2vgf Structure and Function of Human Erythrocyte Pyruvate Kinase. Molecular Basis of Nonspherocytic Hemolytic Anemia.
Resolution	2.75 Å
Binding residue (original residue number in PDB)	L474 T475 T476 T477 S480 W525 R532 G557 R559 P560 G561 S562 G563 Y564 T565
Binding residue (residue number reindexed from 1)	L413 T414 T415 T416 S419 W464 R471 G496 R498 P499 G500 S501 G502 Y503 T504
Annotation score	1

Enzymatic activity

Catalytic site (original residue number in PDB)	R116 R163 K313 T371
Catalytic site (residue number reindexed from 1)	R60 R107 K252 T310
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:0005515	protein binding
GO:0005524	ATP binding
GO:0016301	kinase activity
GO:0030955	potassium ion binding
GO:0046872	metal ion binding
GO:0048029	monosaccharide binding

	Biological Process
GO:0001666	response to hypoxia
GO:0006096	glycolytic process
GO:0007584	response to nutrient
GO:0009749	response to glucose
GO:0010038	response to metal ion
GO:0016310	phosphorylation
GO:0032869	cellular response to insulin stimulus
GO:0033198	response to ATP
GO:0042866	pyruvate biosynthetic process
GO:0051591	response to cAMP
GO:0071872	cellular response to epinephrine stimulus

	Cellular Component
GO:0005737	cytoplasm
GO:0005829	cytosol
GO:0070062	extracellular exosome

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Molecular Function

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Cellular Component

External links

PDB	RCSB:2vgf, PDBe:2vgf, PDBj:2vgf
PDBsum	2vgf
PubMed	11960989
UniProt	P30613\|KPYR_HUMAN Pyruvate kinase PKLR (Gene Name=PKLR)

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