Structure of PDB 5dj3 Chain A Binding Site BS01

Receptor Information

>5dj3 Chain A (length=351) Species: 141454 (Streptomyces wadayamensis)

LNIADGHARQALSPGQQKIVNELPVLWAESEQRPVQQIESEAHQAYFTLL
GQHGYPAEPGRVLSCYSSSVSMEILARSLSASVDRVALVHPTFDNIADLL
RGNGLDLVPVEEDALHGADLSAELLSSVGCVFVTTPNNPTGRVLAEERLR
RLAEQCAEHGTVLALDTSFRGFDAAAHYDHYAVLQEAGCRWVVIEDTGKL
WPTLDLKAGLLVFSEDIGLPVEKIYSDILLGVSPLILALIREFSRDAADG
GLADLHAFILHNRSVVRRALAGVEGVSFPDPESRSSVERVAFAGRTGTEV
WEELQRHHVFALPCRQFHWAEPSDGDHMVRIALSRSTEPLEKSVQVLRTV
L

Ligand information

• Ligand ID: 5DK
• InChI: InChI=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
• InChIKey: PFHOMURYEGODJI-WZZUDYRYSA-N
• SMILES:
  OpenEye OEToolkits 1.9.2: Cc1c(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 12.01: c1(C)ncc(c(c1O)/C=N/C(CCCN/C(N)=N)C(O)=O)COP(O)(O)=O
  CACTVS 3.385: Cc1ncc(CO[P](O)(O)=O)c(C=N[C@H](CCCNC(N)=N)C(O)=O)c1O
  CACTVS 3.385: Cc1ncc(CO[P](O)(O)=O)c(C=N[CH](CCCNC(N)=N)C(O)=O)c1O
• Formula: C14 H22 N5 O7 P
• Name: (E)-N~2~-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-D-arginine;
  PLP-DArg
• ZINC: ZINC000263620882
• PDB chain: 5dj3 Chain A Residue 500

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5dj3 Streptomyces wadayamensis MppP Is a Pyridoxal 5'-Phosphate-Dependent l-Arginine alpha-Deaminase, gamma-Hydroxylase in the Enduracididine Biosynthetic Pathway.
• Resolution: 2.227 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 score: 1

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

External links

• PDB: RCSB:5dj3, PDBe:5dj3, PDBj:5dj3
• PDBsum: 5dj3
• PubMed: 26551990
• UniProt: A0A0X1KHF5