Structure of PDB 3kp1 Chain D Binding Site BS01

Receptor Information
>3kp1 Chain D (length=726) Species: 1511 (Acetoanaerobium sticklandii) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LRVNEKLDVENILKDLDKYTPKRRGWTWRQPAENLQMGPFIYKDASTPLE
NSVALPSAKYFGDIDPQPLPVITTEIASGRFEDDIRRMRMAAWHGADHIM
VIRTAGQSHYDGLIEGTPQGIGGVPITRKQVRAQRKALDLIEEEVGRPIN
YHSYVSGVAGPDIAVMFAEEGVNGAHQDPQYNVLYRNINMIRSFIDACES
KTIMAWADMAQIDGAHNANATAREAWKVMPELMVQHALNSIFSLKVGMKK
SNICLSTVPPTAPPAPSMYLDLPYAVALREMFEGYRMRAQMNTKYMEAST
REATVTHVLNLLISKLTRADIQSTITPDEGRNVPWHIYNIEACDTAKQAL
IGMDGLMDMVQLKREGVLGDTVRELKERAVLFMEEIIEAGGYFNAVEQGF
FVDSGYYPERNGDGIARQINGGIGAGTVFERDEDYMAPVTAHFGYNNVKQ
YDEALVSEPSKLIDGCTLEVPEKIVYIDELDENDNVNVRMEETKEFRSMI
KPEVEWQADGTVLLTMFLPTSKRVAEFAAIEFAKKMNLEEVEVINREVMQ
EAEGTRIELKGRVPFSIDINSLVIPPILSEDEIREDIEKTPLKIVAATVG
EDEHSVGLREVIDIKHGGIEKYGVEVHYLGTSVPVEKLVDAAIELKADAI
LASTIISHDDIHYKNMKRIHELAVEKGIRDKIMIGCGGTQVTPEVAVKQG
VDAGFGRGSKGIHVATFLVKKRREMR
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 chain3kp1 Chain B Residue 1802 [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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PDB3kp1 Large-scale domain dynamics and adenosylcobalamin reorientation orchestrate radical catalysis in ornithine 4,5-aminomutase.
Resolution2.01 Å
Binding residue
(original residue number in PDB)		R109 G112 Q113 S114 Y160 S162 Y187 R192 H225 N226
Binding residue
(residue number reindexed from 1)		R103 G106 Q107 S108 Y154 S156 Y181 R186 H216 N217
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) Y187 H225 R297 K629
Catalytic site (residue number reindexed from 1) Y181 H216 R288 K615
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:3kp1, PDBe:3kp1, PDBj:3kp1
PDBsum3kp1
PubMed20106986
UniProtE3PY95|OAME_ACESD D-ornithine 4,5-aminomutase subunit beta (Gene Name=oraE)

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