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2JFG

Crystal structure of MurD ligase in complex with UMA and ADP

Functional Information from GO Data
ChainGOidnamespacecontents
A0005515molecular_functionprotein binding
A0005524molecular_functionATP binding
A0005737cellular_componentcytoplasm
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 Residues4
DetailsBINDING SITE FOR RESIDUE SO4 A1442
ChainResidue
AHIS309
AASN310
ASER438
AHIS439

site_idAC2
Number of Residues34
DetailsBINDING SITE FOR RESIDUE UMA A1440
ChainResidue
AARG37
ASER71
APRO72
AGLY73
AGLY137
AASN138
AGLY140
ASER159
AGLN162
AHIS183
ALEU416
AHOH2021
AHOH2111
AHOH2142
AHOH2210
AHOH2249
AHOH2259
AHOH2359
AHOH2471
AHOH2472
AHOH2473
AHOH2474
AHOH2475
AHOH2476
AHOH2477
AHOH2478
AHOH2479
AHOH2480
AHOH2481
AGLY14
ALEU15
ATHR16
AASP35
ATHR36

site_idAC3
Number of Residues19
DetailsBINDING SITE FOR RESIDUE ADP A1441
ChainResidue
AASN113
AGLY114
ALYS115
ASER116
ATHR117
AGLU157
AASN178
AHIS267
AASN271
AARG302
AASP317
ALYS319
AALA320
ASER325
AALA328
AHOH2161
AHOH2482
AHOH2483
AHOH2484

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
ASER112

Catalytic Information from CSA
site_idCSA1
Number of Residues1
DetailsAnnotated By Reference To The Literature 1p3d
ChainResidueDetails
ALYS115

site_idCSA2
Number of Residues3
DetailsAnnotated By Reference To The Literature 1p3d
ChainResidueDetails
AASN138
AHIS183
ALYS115

site_idMCSA1
Number of Residues3
DetailsM-CSA 317
ChainResidueDetails
ASER116activator, attractive charge-charge interaction, electrostatic stabiliser, hydrogen bond donor, increase electrophilicity
AILE139electrostatic stabiliser, hydrogen bond donor, steric role
AMET184hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, steric role

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PDB entries from 2024-07-24

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