Structure of PDB 5ofy Chain A Binding Site BS01

Receptor Information
>5ofy Chain A (length=384) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KLLVTPPKALLKPLSIPNQLLGPGPSNLPPRIMAAGGLQMIGSMSKDMYQ
IMDEIKEGIQYVFQTRNPLTLVISGSGHCALEAALVNVLEPGDSFLVGAN
GIWGQRAVDIGERIGARVHPMTKDPGGHYTLQEVEEGLAQHKPVLLFLTH
GESSTGVLQPLDGFGELCHRYKCLLLVNSVASLGGTPLYMDRQGIDILYS
GSQKALNAPPGTSLISFSDKAKKKMYSRKTKPFSFYLDIKWLANFWGCDD
QPRMYHHTIPVISLYSLRESLALIAEQGLENSWRQHREAAAYLHGRLQAL
GLQLFVKDPALRLPTVTTVAVPAGYDWRDIVSYVIDHFDIEIMGGLGPST
GKVLRIGLLGCNATRENVDRVTEALRAALQHCPK
Ligand information
Ligand IDPLP
InChIInChI=1S/C8H10NO6P/c1-5-8(11)7(3-10)6(2-9-5)4-15-16(12,13)14/h2-3,11H,4H2,1H3,(H2,12,13,14)
InChIKeyNGVDGCNFYWLIFO-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.341Cc1ncc(CO[P](O)(O)=O)c(C=O)c1O
OpenEye OEToolkits 1.5.0Cc1c(c(c(cn1)COP(=O)(O)O)C=O)O
ACDLabs 10.04O=P(O)(O)OCc1cnc(c(O)c1C=O)C
FormulaC8 H10 N O6 P
NamePYRIDOXAL-5'-PHOSPHATE;
VITAMIN B6 Phosphate
ChEMBLCHEMBL82202
DrugBankDB00114
ZINCZINC000001532514
PDB chain5ofy Chain A Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5ofy Radiation damage at the active site of human alanine:glyoxylate aminotransferase reveals that the cofactor position is finely tuned during catalysis.
Resolution2.8 Å
Binding residue
(original residue number in PDB)		S81 G82 H83 W108 S158 N183 V185 A186 Q208 K209
Binding residue
(residue number reindexed from 1)		S76 G77 H78 W103 S153 N178 V180 A181 Q203 K204
Annotation score1
Enzymatic activity
Enzyme Commision number 2.6.1.44: alanine--glyoxylate transaminase.
2.6.1.51: serine--pyruvate transaminase.
Gene Ontology
Molecular Function
GO:0004760 L-serine-pyruvate transaminase activity
GO:0005515 protein binding
GO:0008453 alanine-glyoxylate transaminase activity
GO:0008483 transaminase activity
GO:0016597 amino acid binding
GO:0030170 pyridoxal phosphate binding
GO:0042802 identical protein binding
GO:0042803 protein homodimerization activity
Biological Process
GO:0006563 L-serine metabolic process
GO:0007219 Notch signaling pathway
GO:0009436 glyoxylate catabolic process
GO:0019265 glycine biosynthetic process, by transamination of glyoxylate
GO:0019448 L-cysteine catabolic process
GO:0042853 L-alanine catabolic process
GO:0046487 glyoxylate metabolic process
GO:0046724 oxalic acid secretion
Cellular Component
GO:0005777 peroxisome
GO:0005782 peroxisomal matrix
GO:0005829 cytosol
GO:0043231 intracellular membrane-bounded organelle

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5ofy, PDBe:5ofy, PDBj:5ofy
PDBsum5ofy
PubMed28916765
UniProtP21549|AGT1_HUMAN Alanine--glyoxylate aminotransferase (Gene Name=AGXT)

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