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5NRI

Crystal structure of Burkholderia pseudomallei D-alanine-D-alanine ligase in complex with AMP and D-Ala-D-Ala

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
Functional Information from PDB Data
site_idAC1
Number of Residues16
Detailsbinding site for residue AMP A 401
ChainResidue
ALYS104
APHE214
ATYR215
AGLU275
AHOH602
AHOH635
AHOH648
AHOH665
APRO119
APHE146
ALYS148
AGLU184
ALYS185
ASER186
AILE187
AGLU192

site_idAC2
Number of Residues7
Detailsbinding site for residue MG A 404
ChainResidue
AHIS70
AHOH501
AHOH505
AHOH642
AHOH683
AHOH712
AHOH850

site_idAC3
Number of Residues9
Detailsbinding site for residue SO4 A 405
ChainResidue
AARG293
AGLY298
ATYR299
AHOH570
AHOH593
AHOH616
AHOH639
AHOH756
BARG293

site_idAC4
Number of Residues6
Detailsbinding site for residue EDO A 406
ChainResidue
AGLN112
APHE121
AHOH510
AHOH625
AHOH659
BGLN113

site_idAC5
Number of Residues2
Detailsbinding site for residue EDO A 407
ChainResidue
AHIS45
AHOH528

site_idAC6
Number of Residues2
Detailsbinding site for residue EDO A 408
ChainResidue
AARG126
ALYS179

site_idAC7
Number of Residues7
Detailsbinding site for residue SO4 B 401
ChainResidue
AARG293
AHOH630
AHOH942
BLYS290
BHOH532
BHOH605
BHOH630

site_idAC8
Number of Residues5
Detailsbinding site for residue EDO B 402
ChainResidue
BALA240
BARG244
BEDO403
BHOH506
BHOH609

site_idAC9
Number of Residues6
Detailsbinding site for residue EDO B 403
ChainResidue
BALA236
BALA237
BEDO402
BHOH515
BHOH520
BHOH543

site_idAD1
Number of Residues17
Detailsbinding site for residue AMP B 404
ChainResidue
BLYS104
BPHE146
BLYS148
BSER155
BVAL158
BGLU184
BLYS185
BSER186
BILE187
BGLU192
BPHE214
BTYR215
BLEU274
BGLU275
BHOH531
BHOH565
BHOH644

site_idAD2
Number of Residues10
Detailsbinding site for residue SO4 B 405
ChainResidue
BHIS70
BTYR221
BARG260
BASN277
BPRO280
BGLY281
BHOH559
BHOH569
BHOH608
BHOH664

site_idAD3
Number of Residues9
Detailsbinding site for residue PGE B 406
ChainResidue
BARG293
BGLY298
BTYR299
BSER300
BGLU301
BHOH502
BHOH516
BHOH526
BHOH578

site_idAD4
Number of Residues2
Detailsbinding site for residue EDO B 407
ChainResidue
AGLN112
BGLN113

site_idAD5
Number of Residues3
Detailsbinding site for residue EDO B 408
ChainResidue
BHOH631
BHOH682
BARG207

site_idAD6
Number of Residues8
Detailsbinding site for residue EDO B 409
ChainResidue
BVAL25
BSER29
BALA68
BLEU69
BHIS70
BALA279
BPRO280
BHOH545

site_idAD7
Number of Residues7
Detailsbinding site for Di-peptide DAL A 402 and DAL A 403
ChainResidue
AHIS70
AARG260
AASN277
AGLY281
ASER286
ALEU287
AHOH523

Functional Information from PROSITE/UniProt
site_idPS00843
Number of Residues12
DetailsDALA_DALA_LIGASE_1 D-alanine--D-alanine ligase signature 1. HGgyGENGqIQG
ChainResidueDetails
AHIS70-GLY81

site_idPS00844
Number of Residues29
DetailsDALA_DALA_LIGASE_2 D-alanine--D-alanine ligase signature 2. LgctDwGRADFMldaagnpy....FlEVNTaPG
ChainResidueDetails
ALEU253-GLY281

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues8
DetailsBINDING: BINDING => ECO:0000255|HAMAP-Rule:MF_00047
ChainResidueDetails
AGLU275
AASN277
BVAL138
BASP262
BGLU275
BASN277
AVAL138
AASP262

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PDB entries from 2024-05-15

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