Structure of PDB 6jil Chain B Binding Site BS01

Receptor Information
>6jil Chain B (length=298) Species: 1914 (Streptomyces lavendulae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MGILALVTDAVSLPIDYDMPPLLEACRTVGITAEVCDWEDGTVDWSRFEA
VVFRSPWTWAERQAEFLAFCERVSHVTRLITPMPLVRWALDKRYLADLAA
HGVPVIPTTVVAPGSDALAAVRDFLAARPEAREFVVKPTDGCYSKDVQRY
QRSLAEPASRHVARLLANGSHVILQPYVESVDRHGETDLTFFDGVYSHAI
HKGAMLMPDGTVHVPTLDFRQARDADEDQRAVAAAALAASVAHLGLDLPL
VCGRVDLVRGADGSPMVLEMELCEPSLNLTFSEDGALRFAQALAERLK
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 chain6jil Chain B Residue 404 [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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PDB6jil Cyclization mechanism catalyzed by an ATP-grasp enzyme essential for d-cycloserine biosynthesis.
Resolution2.32 Å
Binding residue
(original residue number in PDB)		K92 V135 K137 C142 Y143 S144 Q175 Y177 V178 V181 E186 M205 L206 L268 E269
Binding residue
(residue number reindexed from 1)		K92 V135 K137 C142 Y143 S144 Q175 Y177 V178 V181 E186 M205 L206 L268 E269
Annotation score5
Enzymatic activity
Enzyme Commision number 6.3.3.5: O-ureido-D-serine cyclo-ligase.
Gene Ontology
Molecular Function
GO:0003824 catalytic activity
GO:0005524 ATP binding
GO:0016874 ligase activity
GO:0016882 cyclo-ligase activity
GO:0046872 metal ion binding
Biological Process
GO:0017000 antibiotic biosynthetic process

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Molecular Function
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Biological Process
External links
PDB RCSB:6jil, PDBe:6jil, PDBj:6jil
PDBsum6jil
PubMed31793174
UniProtD2Z030|DCSG_STRLA Cycloserine biosynthesis protein DcsG (Gene Name=dcsG)

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