Structure of PDB 1e4e Chain B Binding Site BS01

Receptor Information
>1e4e Chain B (length=340) Species: 1352 (Enterococcus faecium) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NRIKVAILFGGCSEEHDVSVKSAIEIAANINKEKYEPLYIGITKSGVWKM
CEKPCAEWENENCYSAVLSPDKKMHGLLVKKNHEYEINHVDVAFSALHGK
SGEDGSIQGLFELSGIPFVGCDIQSSAICMDKSLTYIVAKNAGIATPAFW
VINKDDRPVAATFTYPVFVKPARSGSSFGVKKVNSADELDYAIESARQYD
SKILIEQAVSGCEVGCAVLGNSAALVVGEVDQIRLQYGIFRIHQEVEPEK
GSENAVITVPADLSAEERGRIQETVKKIYKTLGCRGLARVDMFLQDRGRI
VLNEVNTLPGFTSYSRYPRMMAAAGISLPELIDRLIVLAL
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 chain1e4e Chain B Residue 350 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB1e4e The molecular basis of vancomycin resistance in clinically relevant Enterococci: crystal structure of D-alanyl-D-lactate ligase (VanA).
Resolution2.5 Å
Binding residue
(original residue number in PDB)		K133 F169 K171 G176 S178 E207 A209 V210 E214 F241 F294 N304 E305
Binding residue
(residue number reindexed from 1)		K132 F168 K170 G175 S177 E206 A208 V209 E213 F240 F293 N303 E304
Annotation score5
Enzymatic activity
Catalytic site (original residue number in PDB) E16 V19 K22 H99 S177 H244 V247 E250 R290 D292 E305 N307 G311 Y315
Catalytic site (residue number reindexed from 1) E15 V18 K21 H98 S176 H243 V246 E249 R289 D291 E304 N306 G310 Y314
Enzyme Commision number 6.1.2.1: D-alanine--(R)-lactate ligase.
Gene Ontology
Molecular Function
GO:0003824 catalytic activity
GO:0005524 ATP binding
GO:0008716 D-alanine-D-alanine ligase activity
GO:0016874 ligase activity
GO:0046872 metal ion binding
Biological Process
GO:0008360 regulation of cell shape
GO:0009252 peptidoglycan biosynthetic process
GO:0046677 response to antibiotic
GO:0071555 cell wall organization
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0005886 plasma membrane

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:1e4e, PDBe:1e4e, PDBj:1e4e
PDBsum1e4e
PubMed10908650
UniProtP25051|VANA_ENTFC Vancomycin/teicoplanin A-type resistance protein VanA (Gene Name=vanA)

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