Structure of PDB 3kox Chain D Binding Site BS02

Receptor Information
>3kox Chain D (length=728) Species: 1511 (Acetoanaerobium sticklandii) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LQLRVNEKLDVENILKDLDKYTPKRRGWTWRQPAENLQMGPFIYKDASTP
LENSVALPSAKYFGDIDPQPLPVITTEIASGRFEDDIRRMRMAAWHGADH
IMVIRTAGQSHYDGLIEGTPQGIGGVPITRKQVRAQRKALDLIEEEVGRP
INYHSYVSGVAGPDIAVMFAEEGVNGAHQDPQYNVLYRNINMIRSFIDAC
ESKTIMAWADMAQIDGAHNANATAREAWKVMPELMVQHALNSIFSLKVGM
KKSNICLSTVPPTAPPAPSMYLDLPYAVALREMFEGYRMRAQMNTKYMEA
STREATVTHVLNLLISKLTRADIQSTITPDEGRNVPWHIYNIEACDTAKQ
ALIGMDGLMDMVQLKREGVLGDTVRELKERAVLFMEEIIEAGGYFNAVEQ
GFFVDSGYYPERNGDGIARQINGGIGAGTVFERDEDYMAPVTAHFGYNNV
KQYDEALVSEPSKLIDGCTLEVPEKIVYIDELDENDNVNVRMEETKEFRS
MIKPEVEWQADGTVLLTMFLPTSKRVAEFAAIEFAKKMNLEEVEVINREV
MQEAEGTRIELKGRVPFSIDINSLVIPPILSEDEIREDIEKTPLKIVAAT
VGEDEHSVGLREVIDIKHGGIEKYGVEVHYLGTSVPVEKLVDAAIELKAD
AILASTIISHDDIHYKNMKRIHELAVEKGIRDKIMIGCGGTQVTPEVAVK
QGVDAGFGRGSKGIHVATFLVKKRREMR
Ligand information
Ligand IDZ98
InChIInChI=1S/C12H18N3O7P/c1-7-11(16)9(5-14-3-2-10(13)12(17)18)8(4-15-7)6-22-23(19,20)21/h4-5,10,16H,2-3,6,13H2,1H3,(H,17,18)(H2,19,20,21)/b14-5-/t10-/m0/s1
InChIKeyBBWBZEWRKQXPMM-YXBHYIBOSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0Cc1c(c(c(cn1)COP(=O)(O)O)C=NCCC(C(=O)O)N)O
CACTVS 3.352Cc1ncc(CO[P](O)(O)=O)c(C=NCC[CH](N)C(O)=O)c1O
CACTVS 3.352Cc1ncc(CO[P](O)(O)=O)c(C=NCC[C@H](N)C(O)=O)c1O
OpenEye OEToolkits 1.7.0Cc1c(c(c(cn1)COP(=O)(O)O)/C=N\CC[C@@H](C(=O)O)N)O
FormulaC12 H18 N3 O7 P
Name(2S)-2-amino-4-{[(1Z)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene]amino}butanoic acid
ChEMBL
DrugBank
ZINCZINC000058649364
PDB chain3kox Chain D Residue 767 [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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PDB3kox Large-scale domain dynamics and adenosylcobalamin reorientation orchestrate radical catalysis in ornithine 4,5-aminomutase.
Resolution2.4 Å
Binding residue
(original residue number in PDB)		E81 R109 G112 Q113 S114 Y160 S162 H182 Y187 R192 H225 N226 R297
Binding residue
(residue number reindexed from 1)		E77 R105 G108 Q109 S110 Y156 S158 H178 Y183 R188 H218 N219 R290
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) Y187 H225 R297 K629
Catalytic site (residue number reindexed from 1) Y183 H218 R290 K617
Enzyme Commision number 5.4.3.5: D-ornithine 4,5-aminomutase.
Gene Ontology
Molecular Function
GO:0003824 catalytic activity
GO:0016853 isomerase activity
GO:0031419 cobalamin binding
GO:0046872 metal ion binding
GO:0046983 protein dimerization activity
GO:0047831 D-ornithine 4,5-aminomutase activity

View graph for
Molecular Function
External links
PDB RCSB:3kox, PDBe:3kox, PDBj:3kox
PDBsum3kox
PubMed20106986
UniProtE3PY95|OAME_ACESD D-ornithine 4,5-aminomutase subunit beta (Gene Name=oraE)

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