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5C1O

Crystal structure of AMP-PNP complexed D-alanine-D-alanine ligase(DDL) from Yersinia pestis

Functional Information from GO Data
ChainGOidnamespacecontents
A0003824molecular_functioncatalytic activity
A0005524molecular_functionATP binding
A0005737cellular_componentcytoplasm
A0005829cellular_componentcytosol
A0008360biological_processregulation of cell shape
A0008716molecular_functionD-alanine-D-alanine ligase activity
A0009252biological_processpeptidoglycan biosynthetic process
A0016874molecular_functionligase activity
A0046872molecular_functionmetal ion binding
A0071555biological_processcell wall organization
B0003824molecular_functioncatalytic activity
B0005524molecular_functionATP binding
B0005737cellular_componentcytoplasm
B0005829cellular_componentcytosol
B0008360biological_processregulation of cell shape
B0008716molecular_functionD-alanine-D-alanine ligase activity
B0009252biological_processpeptidoglycan biosynthetic process
B0016874molecular_functionligase activity
B0046872molecular_functionmetal ion binding
B0071555biological_processcell wall organization
C0003824molecular_functioncatalytic activity
C0005524molecular_functionATP binding
C0005737cellular_componentcytoplasm
C0005829cellular_componentcytosol
C0008360biological_processregulation of cell shape
C0008716molecular_functionD-alanine-D-alanine ligase activity
C0009252biological_processpeptidoglycan biosynthetic process
C0016874molecular_functionligase activity
C0046872molecular_functionmetal ion binding
C0071555biological_processcell wall organization
D0003824molecular_functioncatalytic activity
D0005524molecular_functionATP binding
D0005737cellular_componentcytoplasm
D0005829cellular_componentcytosol
D0008360biological_processregulation of cell shape
D0008716molecular_functionD-alanine-D-alanine ligase activity
D0009252biological_processpeptidoglycan biosynthetic process
D0016874molecular_functionligase activity
D0046872molecular_functionmetal ion binding
D0071555biological_processcell wall organization
Functional Information from PDB Data
site_idAC1
Number of Residues15
Detailsbinding site for residue ANP A 401
ChainResidue
ALYS97
ATYR210
ATYR212
AMET259
ALEU269
AGLU270
AMG403
AILE142
ALYS144
AMET154
AGLU180
ALYS181
ATRP182
ALEU183
AGLU187

site_idAC2
Number of Residues6
Detailsbinding site for residue NA A 402
ChainResidue
AGLU68
ASER91
ATHR94
AMET95
ATHR273
AHOH504

site_idAC3
Number of Residues2
Detailsbinding site for residue MG A 403
ChainResidue
AGLU270
AANP401

site_idAC4
Number of Residues12
Detailsbinding site for residue ANP B 401
ChainResidue
BLYS97
BLYS144
BGLU148
BSER151
BMET154
BGLU180
BLYS181
BLEU183
BGLU187
BMET259
BGLU270
BMG403

site_idAC5
Number of Residues6
Detailsbinding site for residue NA B 402
ChainResidue
BGLU68
BSER91
BTHR94
BMET95
BTHR273
BHOH505

site_idAC6
Number of Residues4
Detailsbinding site for residue MG B 403
ChainResidue
BLYS97
BGLU148
BGLU270
BANP401

site_idAC7
Number of Residues2
Detailsbinding site for residue NA B 404
ChainResidue
BHIS265
CHIS280

site_idAC8
Number of Residues17
Detailsbinding site for residue ANP C 401
ChainResidue
CLYS97
CILE142
CLYS144
CGLU148
CSER151
CMET154
CGLU180
CLYS181
CTRP182
CLEU183
CGLU187
CPHE209
CTYR210
CLYS215
CMET259
CGLU270
CMG403

site_idAC9
Number of Residues6
Detailsbinding site for residue NA C 402
ChainResidue
CGLU68
CSER91
CTHR94
CMET95
CTHR273
CHOH507

site_idAD1
Number of Residues3
Detailsbinding site for residue MG C 403
ChainResidue
CGLU148
CGLU270
CANP401

site_idAD2
Number of Residues15
Detailsbinding site for residue ANP D 401
ChainResidue
DLYS97
DILE142
DLYS144
DGLU148
DSER151
DMET154
DGLU180
DLYS181
DTRP182
DLEU183
DGLU187
DPHE209
DMET259
DGLU270
DMG403

site_idAD3
Number of Residues5
Detailsbinding site for residue NA D 402
ChainResidue
DGLU68
DSER91
DTHR94
DMET95
DTHR273

site_idAD4
Number of Residues3
Detailsbinding site for residue MG D 403
ChainResidue
DGLU148
DGLU270
DANP401

Functional Information from PROSITE/UniProt
site_idPS00843
Number of Residues12
DetailsDALA_DALA_LIGASE_1 D-alanine--D-alanine ligase signature 1. HGrgGEDGtLQG
ChainResidueDetails
AHIS63-GLY74

site_idPS00844
Number of Residues29
DetailsDALA_DALA_LIGASE_2 D-alanine--D-alanine ligase signature 2. LdcsGwGRVDVMqdrdghfy....LlEVNTsPG
ChainResidueDetails
ALEU248-GLY276

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues16
DetailsBINDING: BINDING => ECO:0000255|HAMAP-Rule:MF_00047
ChainResidueDetails
BVAL134
BASP257
BGLU270
BASN272
CVAL134
CASP257
CGLU270
CASN272
DVAL134
DASP257
DGLU270
DASN272
AVAL134
AASP257
AGLU270
AASN272

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PDB entries from 2024-05-15

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