Structure of PDB 3vmm Chain A Binding Site BS03

Receptor Information
>3vmm Chain A (length=471) Species: 1423 (Bacillus subtilis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ERKTVLVIADLGGCPPHMFYKSAAEKYNLVSFIPRPFAITASHAALIEKY
SVAVIKDKDYFKSLADFEHPDSIYWAHEDHNKPEEEVVEQIVKVAEMFGA
DAITTNNELFIAPMAKACERLGLRGAGVQAAENARDKNKMRDAFNKAGVK
SIKNKRVTTLEDFRAALEEIGTPLILKPTYLASSIGVTLITDTETAEDEF
NRVNDYLKSINVPKAVTFEAPFIAEEFLQGEYGDWYQTEGYSDYISIEGI
MADGEYFPIAIHDKTPQIGFTETSHITPSILDEEAKKKIVEAAKKANEGL
GLQNCATHTEIKLMKNREPGLIESAARFAGWNMIPNIKKVFGLDMAQLLL
DVLCFGKDADLPDGLLDQEPYYVADCHLYPQHFKQNGQIPETAEDLVIEA
IDIPDGLLKGDTEIVSFSAAAPGTSVDLTLFEAFNSIAAFELKGSNSQDV
AESIRQIQQHAKLTAKYVLPV
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 chain3vmm Chain A Residue 503 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3vmm Structural and enzymatic characterization of BacD, an l-amino acid dipeptide ligase from Bacillus subtilis
Resolution2.5 Å
Binding residue
(original residue number in PDB)		K138 I176 K178 A183 S185 F228 L229 Q268 F271 I323 E324
Binding residue
(residue number reindexed from 1)		K137 I175 K177 A182 S184 F227 L228 Q267 F270 I322 E323
Annotation score5
Enzymatic activity
Enzyme Commision number 6.3.2.49: L-alanine--L-anticapsin ligase.
Gene Ontology
Molecular Function
GO:0003824 catalytic activity
GO:0005524 ATP binding
GO:0016874 ligase activity
GO:0034026 L-amino-acid alpha-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:3vmm, PDBe:3vmm, PDBj:3vmm
PDBsum3vmm
PubMed22407814
UniProtP39641|BACD_BACSU Alanine--anticapsin ligase (Gene Name=bacD)

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