Structure of PDB 5hdm Chain A Binding Site BS01

Receptor Information
>5hdm Chain A (length=428) Species: 3702 (Arabidopsis thaliana) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SFSLQKSEEAFNAAKNLMPGGVNSPVRAFKSVGGQPVLIDSVKGSKMWDI
DGNEYIDYVGSWGPAIIGHADDEVLAALAETMKKGTSFGAPCLLENVLAE
MVISAVPSIEMVRFVNSGTEACMGVLRLARAFTNKEKFIKFEGCYHGHAN
AFLVKAGSGVATLGLPDSPGVPKAATSDTLTAPYNDLEAVEKLFAAHKGE
ISAVILEPVVGNSGFIPPTPEFINGLRQLTKDNGVLLIFDEVMTGFRLAY
GGAQEYFGITPDLTTLGKIIGGGLPVGAYGGRRDIMEMVAPAGPMYQAGT
LSGNPLAMTAGIHTLKRLKQAGTYEYLDKITKELTNGILEAGKKTGHPMC
GGYISGMFGFFFAEGPVYNFADSKKSDTEKFGRFFRGMLEEGVYFAPSQF
EAGFTSLAHTPEDIQLTIAAAERVLSRI
Ligand information
Ligand IDPMP
InChIInChI=1S/C8H13N2O5P/c1-5-8(11)7(2-9)6(3-10-5)4-15-16(12,13)14/h3,11H,2,4,9H2,1H3,(H2,12,13,14)
InChIKeyZMJGSOSNSPKHNH-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O=P(O)(O)OCc1cnc(c(O)c1CN)C
OpenEye OEToolkits 1.5.0Cc1c(c(c(cn1)COP(=O)(O)O)CN)O
CACTVS 3.341Cc1ncc(CO[P](O)(O)=O)c(CN)c1O
FormulaC8 H13 N2 O5 P
Name4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE;
PYRIDOXAMINE-5'-PHOSPHATE
ChEMBLCHEMBL1235353
DrugBankDB02142
ZINCZINC000001532708
PDB chain5hdm Chain A Residue 500 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5hdm Crystal structure of glutamate-1-semialdehyde-2,1-aminomutase from Arabidopsis thaliana.
Resolution1.25 Å
Binding residue
(original residue number in PDB)		G124 T125 Y151 G153 E213 N218 D246 V248 K274
Binding residue
(residue number reindexed from 1)		G118 T119 Y145 G147 E207 N212 D240 V242 K268
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) V28 Y151 E213 D246 M249 K274 A408
Catalytic site (residue number reindexed from 1) V22 Y145 E207 D240 M243 K268 A402
Enzyme Commision number 5.4.3.8: glutamate-1-semialdehyde 2,1-aminomutase.
Gene Ontology
Molecular Function
GO:0008483 transaminase activity
GO:0016853 isomerase activity
GO:0030170 pyridoxal phosphate binding
GO:0042286 glutamate-1-semialdehyde 2,1-aminomutase activity
GO:0042803 protein homodimerization activity
Biological Process
GO:0006782 protoporphyrinogen IX biosynthetic process
GO:0015995 chlorophyll biosynthetic process
GO:0033014 tetrapyrrole biosynthetic process
Cellular Component
GO:0005829 cytosol
GO:0009507 chloroplast
GO:0009536 plastid
GO:0009570 chloroplast stroma
GO:0009941 chloroplast envelope
GO:0048046 apoplast

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Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5hdm, PDBe:5hdm, PDBj:5hdm
PDBsum5hdm
PubMed27303897
UniProtP42799|GSA1_ARATH Glutamate-1-semialdehyde 2,1-aminomutase 1, chloroplastic (Gene Name=GSA1)

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