Structure of PDB 4bub Chain A Binding Site BS01

Receptor Information
>4bub Chain A (length=478) Species: 2336 (Thermotoga maritima) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MNISTIVSNLKDLILEVRAPYDLEITGVSNHSSKVKKGDLFICRREIIPE
VMEKGAVAVVVEREIDLDFPYIQVFDSRYFEAKVASLFFEDPWKDVLTFG
VTGTNGKTTTTMMIYHMLTSLGERGSVLTTAVKRILGNSYYDDITTPDAI
TILSAMKENREGGGKFFALEVSSHALVQQRVEGVRFDVGIFTNISRDHLD
FHGTFENYLKAKLHLFDLLKDDGVAVLNESLADAFNRKSRKITFGTSKNA
DYRLGNIEVSWEGTQFVLETPDGLLKVFTRAIGDFNAYNAAAAIAALHQL
GYDPKDLASSLETFTGVEGRFEVVRGAKKIGLNVVVDFAHSPDALEKLLK
NVRKISQGRVIVVFGAGGNSDRGKRPMMSEVASKLADVVILTTDDPRGED
PEQIMEDLIKGIDKRKPYLVLFDRREAIETALTIANRGDSVVIAGRGHER
YQIIDEEKKVPFQDREVVEEIIRDKLKG
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 chain4bub Chain A Residue 1486 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4bub Mreb and Murg as Scaffolds for the Cytoplasmic Steps of Peptidoglycan Biosynthesis
Resolution2.9 Å
Binding residue
(original residue number in PDB)		N112 G113 K114 T115 N200 F292 N296 R327 K354
Binding residue
(residue number reindexed from 1)		N105 G106 K107 T108 N193 F285 N289 R320 K347
Annotation score5
Enzymatic activity
Catalytic site (original residue number in PDB) K114 T115 E165
Catalytic site (residue number reindexed from 1) K107 T108 E158
Enzyme Commision number 6.3.2.37: UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--D-lysine ligase.
6.3.2.7: UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--L-lysine ligase.
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0004326 tetrahydrofolylpolyglutamate synthase activity
GO:0005524 ATP binding
GO:0016874 ligase activity
GO:0016881 acid-amino acid ligase activity
GO:0047482 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate-L-lysine ligase activity
GO:0102195 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--D-lysine ligase activity
Biological Process
GO:0008360 regulation of cell shape
GO:0009058 biosynthetic process
GO:0009252 peptidoglycan biosynthetic process
GO:0009396 folic acid-containing compound biosynthetic process
GO:0046901 tetrahydrofolylpolyglutamate biosynthetic process
GO:0051301 cell division
GO:0071555 cell wall organization
Cellular Component
GO:0005737 cytoplasm

View graph for
Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:4bub, PDBe:4bub, PDBj:4bub
PDBsum4bub
PubMed23826965
UniProtQ9WY79|MURE_THEMA UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--LD-lysine ligase (Gene Name=murE)

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