Structure of PDB 2y68 Chain A

Receptor sequence
>2y68A (length=435) Species: 83333 (Escherichia coli K-12) [Search protein sequence]
ADYQGKNVVIIGLGLTGLSCVDFFLARGVTPRVMDTRMTPPGLDKLPEAV
ERHTGSLNDEWLMAADLIVASPGIALAHPSLSAAADAGIEIVGDIELFCR
EAQAPIVAITGSNGKSTVTTLVGEMAKAAGVNVGVGGNIGLPALMLLDDE
CELYVLELSSFQLETTSSLQAVAATILNVTEDHMDRYPFGLQQYRAAKLR
IYENAKVCVVNADDALTMPIRRCVSFGVNMGDYHLNHQQGETWLRVKGEK
VLNVKEMKLSGQHNYTNALAALALADAAGLPRASSLKALTTFTGLPHRFE
VVLEHNGVRWINDSKATNVGSTEAALNGLHVDGTLHLLLGGDGKSADFSP
LARYLNGDNVRLYCFGRDGAQLAALRPEVAEQTETMEQAMRLLAPRVQPG
DMVLLSPACASLDQFKNFEQRGNEFARLAKELGSH
3D structure
PDB2y68 Structure-based design of a new series of D-glutamic acid based inhibitors of bacterial UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase (MurD).
ChainA
Resolution1.49 Å
3D
structure
Catalytic site residues are labeled in the structure
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Enzymatic activity
Catalytic site (original residue number in PDB) K115 S116 N138 L147 H183
Catalytic site (residue number reindexed from 1) K115 S116 N138 L147 H183
Enzyme Commision number 6.3.2.9: UDP-N-acetylmuramoyl-L-alanine--D-glutamate ligase.
Interaction with ligand
Site
#		 Ligand Ligand
chain		 Binding residues on receptor
(original residue number in PDB)		 Binding residues on receptor
(residue number reindexed from 1)		 Binding affinity
BS01 T04 A G12 D35 T36 R37 S71 G73 F161 H183 K348 A414 S415 N421 F422 G12 D35 T36 R37 S71 G73 F161 H183 K344 A410 S411 N417 F418 MOAD: ic50=253uM
PDBbind-CN: -logKd/Ki=3.60,IC50=253uM
BS02 AZI A A329 N331 L333 A325 N327 L329
BS03 AZI A N363 V364 N359 V360
Gene Ontology
Molecular Function
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0008764 UDP-N-acetylmuramoylalanine-D-glutamate ligase activity
GO:0016874 ligase activity
GO:0016881 acid-amino acid ligase activity
GO:0042802 identical protein binding
Biological Process
GO:0008360 regulation of cell shape
GO:0009058 biosynthetic process
GO:0009252 peptidoglycan biosynthetic process
GO:0051301 cell division
GO:0071555 cell wall organization
Cellular Component
GO:0005737 cytoplasm

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:2y68, PDBe:2y68, PDBj:2y68
PDBsum2y68
PubMed21591605
UniProtP14900|MURD_ECOLI UDP-N-acetylmuramoylalanine--D-glutamate ligase (Gene Name=murD)

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