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2Y68

Structure-based design of a new series of D-glutamic acid-based inhibitors of bacterial MurD ligase

Functional Information from GO Data
ChainGOidnamespacecontents
A0000166molecular_functionnucleotide binding
A0005515molecular_functionprotein binding
A0005524molecular_functionATP binding
A0005737cellular_componentcytoplasm
A0007049biological_processcell cycle
A0008360biological_processregulation of cell shape
A0008764molecular_functionUDP-N-acetylmuramoylalanine-D-glutamate ligase activity
A0009058biological_processbiosynthetic process
A0009252biological_processpeptidoglycan biosynthetic process
A0016874molecular_functionligase activity
A0016881molecular_functionacid-amino acid ligase activity
A0042802molecular_functionidentical protein binding
A0051301biological_processcell division
A0071555biological_processcell wall organization
Functional Information from PDB Data
site_idAC1
Number of Residues22
DetailsBINDING SITE FOR RESIDUE T04 A 500
ChainResidue
AILE11
AALA414
ASER415
AASN421
APHE422
ASO41442
AHOH2166
AHOH2193
AHOH2234
AHOH2439
AHOH2440
AASP35
AHOH2441
AHOH2443
AHOH2447
ATHR36
AARG37
ASER71
AASN138
APHE161
AHIS183
ALYS348

site_idAC2
Number of Residues7
DetailsBINDING SITE FOR RESIDUE DMS A 601
ChainResidue
ALEU163
ATHR166
ASER167
ASER168
ALEU169
AARG200
AGLU203

site_idAC3
Number of Residues6
DetailsBINDING SITE FOR RESIDUE DMS A 604
ChainResidue
AASN7
AARG32
AALA64
AGLU308
AHIS309
AASN310

site_idAC4
Number of Residues2
DetailsBINDING SITE FOR RESIDUE AZI A 700
ChainResidue
AGLN418
APHE419

site_idAC5
Number of Residues4
DetailsBINDING SITE FOR RESIDUE AZI A 701
ChainResidue
AALA329
AASN331
AGLY332
ALEU333

site_idAC6
Number of Residues3
DetailsBINDING SITE FOR RESIDUE AZI A 703
ChainResidue
ALEU339
AASN363
AVAL364

site_idAC7
Number of Residues4
DetailsBINDING SITE FOR RESIDUE AZI A 704
ChainResidue
AALA104
APRO105
AHOH2138
AHOH2444

site_idAC8
Number of Residues8
DetailsBINDING SITE FOR RESIDUE SO4 A 1440
ChainResidue
AASN113
AGLY114
ALYS115
ASER116
ATHR117
AARG302
AHOH2445
AHOH2446

site_idAC9
Number of Residues4
DetailsBINDING SITE FOR RESIDUE SO4 A 1441
ChainResidue
AHIS309
AASN310
ASER438
AHIS439

site_idBC1
Number of Residues7
DetailsBINDING SITE FOR RESIDUE SO4 A 1442
ChainResidue
AGLY14
ALEU15
ATHR16
AT04500
AHOH2447
AHOH2448
AHOH2449

site_idBC2
Number of Residues3
DetailsBINDING SITE FOR RESIDUE SO4 A 1443
ChainResidue
AARG37
AMET38
AGLN170

site_idBC3
Number of Residues1
DetailsBINDING SITE FOR RESIDUE CL A 1444
ChainResidue
AARG395

site_idBC4
Number of Residues3
DetailsBINDING SITE FOR RESIDUE CL A 1445
ChainResidue
ASER56
ALEU57
AHOH2103

Functional Information from PROSITE/UniProt
site_idPS00012
Number of Residues16
DetailsPHOSPHOPANTETHEINE Phosphopantetheine attachment site. GSNGKSTVTTLVGEMA
ChainResidueDetails
AGLY111-ALA126

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues1
DetailsBINDING: BINDING => ECO:0000255
ChainResidueDetails
AGLY111

Catalytic Information from CSA
site_idMCSA1
Number of Residues3
DetailsM-CSA 317
ChainResidueDetails
ALYS115activator, attractive charge-charge interaction, electrostatic stabiliser, hydrogen bond donor, increase electrophilicity
AASN138electrostatic stabiliser, hydrogen bond donor, steric role
AHIS183hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, steric role

218853

PDB entries from 2024-04-24

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