Structure of PDB 3vot Chain B Binding Site BS01

Receptor Information
>3vot Chain B (length=394) Species: 279010 (Bacillus licheniformis DSM 13 = ATCC 14580) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TKRNKNLAIICQNKHLPFIFEEAERLGLKVTFFYNSAEDFPGNLPAVERC
VPLPLFEDEEAAMDVVRQTFVEFPFDGVMTLFEPALPFTAKAAEALNLPG
LPFTTMENCRNKNKTRSILQQNGLNTPVFHEFHTLADLEKLSYPLVVKPV
NGVVRVDDRKELEEAVRKVTGIVAEQFIDGPEFAIETLSIQGNVHVLSIG
YKGNSKGPFFEEGVYIAPAQLKEETRLAIVKEVTGAVSALGIHQGPAHTE
LRLDKDGTPYVIEVGARIGGSGVSHYIVKESTGINFMQLVLQNALKPLES
SEFEGEIRPVRTAGNYIIPVQGSGTFEKIDGLEEVKQRQEVKRVFQFMRR
GAKILPYPHFSGYPGFILTSHHSYEECEAFYRELDDELHIIYQN
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 chain3vot Chain B Residue 501 [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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PDB3vot The structure of L-amino-acid ligase from Bacillus licheniformis
Resolution1.8 Å
Binding residue
(original residue number in PDB)		K113 K151 V161 E198 F200 I201 E205 F233 E273 R275 I285 E286
Binding residue
(residue number reindexed from 1)		K112 K148 V153 E175 F177 I178 E182 F210 E250 R252 I262 E263
Annotation score4
Enzymatic activity
Enzyme Commision number 6.3.2.28: Transferred entry: 6.3.2.49.
Gene Ontology
Molecular Function
GO:0005524 ATP binding
GO:0016874 ligase activity
GO:0046872 metal ion binding

View graph for
Molecular Function
External links
PDB RCSB:3vot, PDBe:3vot, PDBj:3vot
PDBsum3vot
PubMed23090402
UniProtQ65D11

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