Structure of PDB 5dj3 Chain B Binding Site BS01

Receptor Information
>5dj3 Chain B (length=351) Species: 141454 (Streptomyces wadayamensis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LNIADGHARQALSPGQQKIVNELPVLWAESEQRPVQQIESEAHQAYFTLL
GQHGYPAEPGRVLSCYSSSVSMEILARSLSASVDRVALVHPTFDNIADLL
RGNGLDLVPVEEDALHGADLSAELLSSVGCVFVTTPNNPTGRVLAEERLR
RLAEQCAEHGTVLALDTSFRGFDAAAHYDHYAVLQEAGCRWVVIEDTGKL
WPTLDLKAGLLVFSEDIGLPVEKIYSDILLGVSPLILALIREFSRDAADG
GLADLHAFILHNRSVVRRALAGVEGVSFPDPESRSSVERVAFAGRTGTEV
WEELQRHHVFALPCRQFHWAEPSDGDHMVRIALSRSTEPLEKSVQVLRTV
L
Ligand information
Ligand ID5DK
InChIInChI=1S/C14H22N5O7P/c1-8-12(20)10(9(5-18-8)7-26-27(23,24)25)6-19-11(13(21)22)3-2-4-17-14(15)16/h5-6,11,20H,2-4,7H2,1H3,(H,21,22)(H4,15,16,17)(H2,23,24,25)/b19-6+/t11-/m1/s1
InChIKeyPFHOMURYEGODJI-WZZUDYRYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.9.2Cc1c(c(c(cn1)COP(=O)(O)O)C=NC(CCCNC(=N)N)C(=O)O)O
OpenEye OEToolkits 1.9.2[H]/N=C(\N)/NCCC[C@H](C(=O)O)/N=C/c1c(cnc(c1O)C)COP(=O)(O)O
ACDLabs 12.01c1(C)ncc(c(c1O)/C=N/C(CCCN/C(N)=N)C(O)=O)COP(O)(O)=O
CACTVS 3.385Cc1ncc(CO[P](O)(O)=O)c(C=N[C@H](CCCNC(N)=N)C(O)=O)c1O
CACTVS 3.385Cc1ncc(CO[P](O)(O)=O)c(C=N[CH](CCCNC(N)=N)C(O)=O)c1O
FormulaC14 H22 N5 O7 P
Name(E)-N~2~-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-D-arginine;
PLP-DArg
ChEMBL
DrugBank
ZINCZINC000263620882
PDB chain5dj3 Chain B Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB5dj3 Streptomyces wadayamensis MppP Is a Pyridoxal 5'-Phosphate-Dependent l-Arginine alpha-Deaminase, gamma-Hydroxylase in the Enduracididine Biosynthetic Pathway.
Resolution2.227 Å
Binding residue
(original residue number in PDB)		D27 G28 H29 S89 S90 S91 F115 N160 D188 S190 K221 D227 K229 R352
Binding residue
(residue number reindexed from 1)		D5 G6 H7 S67 S68 S69 F93 N138 D166 S168 K199 D205 K207 R330
Annotation score1
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0008483 transaminase activity
GO:0030170 pyridoxal phosphate binding
GO:0046872 metal ion binding
Biological Process
GO:0006520 amino acid metabolic process
GO:0009058 biosynthetic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:5dj3, PDBe:5dj3, PDBj:5dj3
PDBsum5dj3
PubMed26551990
UniProtA0A0X1KHF5

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