Structure of PDB 5vec Chain B Binding Site BS01

Receptor Information
>5vec Chain B (length=564) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SNMVKIVTVKTQAYQDQKPGTSGLRKRVKVFQSSANYAENFIQSIISTVE
PAQRQEATLVVGGDGRFYMKEAIQLIARIAAANGIGRLVIGQNGILSTPA
VSCIIRKIKAIGGIILTASHNPGGPNGDFGIKFNISNGGPAPEAITDKIF
QISKTIEEYAVCPDLKVDLGVLGKQQFDLENKFKPFTVEIVDSVEAYATM
LRSIFDFSALKELLSGPNRLKIRIDAMHGVVGPYVKKILCEELGAPANSA
VNCVPLEDFGGHHPDPNLTYAADLVETMKSGEHDFGAAFDGDGDRNMILG
KHGFFVNPSDSVAVIAANIFSIPYFQQTGVRGFARSMPTSGALDRVASAT
KIALYETPTGWKFFGNLMDASKLSLCGEESFGTGSDHIREKDGLWAVLAW
LSILATRKQSVEDILKDHWQKYGRNFFTRYDYEEVEAEGANKMMKDLEAL
MFDRSFVGKQFSANDKVYTVEKADNFEYSDPVDGSISRNQGLRLIFTDGS
RIVFRLSGTGSAGATILLYIDSYEKDVAKINQDPQVMLAPLISIALKVSQ
LQERTGRTAPTVIT
Ligand information
Ligand IDMG
InChIInChI=1S/Mg/q+2
InChIKeyJLVVSXFLKOJNIY-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04
OpenEye OEToolkits 1.5.0		[Mg+2]
CACTVS 3.341[Mg++]
FormulaMg
NameMAGNESIUM ION
ChEMBL
DrugBankDB01378
ZINC
PDB chain5vec Chain B Residue 603 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5vec A Hotspot for Disease-Associated Variants of Human PGM1 Is Associated with Impaired Ligand Binding and Loop Dynamics.
Resolution2.20002 Å
Binding residue
(original residue number in PDB)		S117 D288 D290 D292
Binding residue
(residue number reindexed from 1)		S119 D290 D292 D294
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) R23 S117 H118 K130 D288 D290 D292 R293 G380
Catalytic site (residue number reindexed from 1) R25 S119 H120 K132 D290 D292 D294 R295 G382
Enzyme Commision number 5.4.2.2: phosphoglucomutase (alpha-D-glucose-1,6-bisphosphate-dependent).
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0004614 phosphoglucomutase activity
GO:0005515 protein binding
GO:0016853 isomerase activity
GO:0016868 intramolecular phosphotransferase activity
GO:0046872 metal ion binding
Biological Process
GO:0005975 carbohydrate metabolic process
GO:0006006 glucose metabolic process
GO:0006094 gluconeogenesis
GO:0006096 glycolytic process
GO:0033499 galactose catabolic process via UDP-galactose
Cellular Component
GO:0005576 extracellular region
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0070062 extracellular exosome
GO:1904724 tertiary granule lumen
GO:1904813 ficolin-1-rich granule lumen

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5vec, PDBe:5vec, PDBj:5vec
PDBsum5vec
PubMed30122451
UniProtP36871|PGM1_HUMAN Phosphoglucomutase-1 (Gene Name=PGM1)

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