Structure of PDB 3vf2 Chain A Binding Site BS03

Receptor Information
>3vf2 Chain A (length=566) Species: 1933 (Streptoalloteichus tenebrarius) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MRVLGLNGWPRDFHDASAALLVDGRIAAFAEEERFTRKKHGYNTAPVQAA
AFCLAQAGLTVDDLDAVAFGWDLPAMYRERLGGWPHSDSEALDILLPRDV
FPRRTDPPLHFVQHHLAHAASAYYFSGEDRGAVLIVDGQGEEECVTLAHA
EGGKITVLDTVPGAWSLGFFYEHVSEYTGLGGDNPGKLMGLAAHGTTVDE
TLSAFAFDSDGYRLNLIDPQARDPEDWDEYSVTERAWFAHLERIYRLPPN
EFVRRYDPAKGRVVRDTRRDPYEYRDLAATAQAALERAVFGLADSVLART
GERTLFVAGGVGLNATMNGKLLTRSTVDKMFVPPVASDIGVSLGAAAAVA
VELGDRIAPMGDTAAWGPEFSPDQVRAALDRTGLAYREPANLEREVAALI
ASGKVVGWAQGRGEVGPRALGQRSLLGSAHSPTMRDHINLRVKDREWWRP
FAPSMLRSVSDQVLEVDADFPYIIMTTKVRAAYAERLPSVVHEDWSTRPQ
TVTEASNPRYHRMLTELGDLVGDPVCLNTSFNDRGEPIVSSPADALLTFS
RLPIDALAVGPYLVTK
Ligand information
Ligand IDADP
InChIInChI=1S/C10H15N5O10P2/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(24-10)1-23-27(21,22)25-26(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKeyXTWYTFMLZFPYCI-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N
FormulaC10 H15 N5 O10 P2
NameADENOSINE-5'-DIPHOSPHATE
ChEMBLCHEMBL14830
DrugBankDB16833
ZINCZINC000012360703
PDB chain3vf2 Chain A Residue 604 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3vf2 The O-Carbamoyltransferase TobZ Catalyzes an Ancient Enzymatic Reaction.
Resolution2.9 Å
Binding residue
(original residue number in PDB)		H14 H118 D137 G138 G168 Y171 E172 P185 G310 N314 S337 D338
Binding residue
(residue number reindexed from 1)		H14 H118 D137 G138 G168 Y171 E172 P185 G310 N314 S337 D338
Annotation score4
Enzymatic activity
Enzyme Commision number 6.1.2.2: nebramycin 5' synthase.
Gene Ontology
Molecular Function
GO:0003824 catalytic activity
GO:0005506 iron ion binding
GO:0005524 ATP binding
GO:0016743 carboxyl- or carbamoyltransferase activity
GO:0016787 hydrolase activity
GO:0016874 ligase activity
GO:0046872 metal ion binding
Biological Process
GO:0009058 biosynthetic process
GO:0017000 antibiotic biosynthetic process
GO:1901121 tobramycin biosynthetic process
GO:1901133 kanamycin biosynthetic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:3vf2, PDBe:3vf2, PDBj:3vf2
PDBsum3vf2
PubMed22383337
UniProtQ70IY1|TOBZ_STRSD nebramycin 5' synthase (Gene Name=tobZ)

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