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5DC2

X-RAY CRYSTAL STRUCTURE OF A ENZYMATICALLY DEGRADED BIAPENEM-ADDUCT OF L,D-TRANSPEPTIDASE 2 FROM MYCOBACTERIUM TUBERCULOSIS

Functional Information from GO Data
ChainGOidnamespacecontents
A0005886cellular_componentplasma membrane
A0008360biological_processregulation of cell shape
A0009252biological_processpeptidoglycan biosynthetic process
A0016020cellular_componentmembrane
A0016740molecular_functiontransferase activity
A0016746molecular_functionacyltransferase activity
A0018104biological_processpeptidoglycan-protein cross-linking
A0046872molecular_functionmetal ion binding
A0071555biological_processcell wall organization
A0071972molecular_functionpeptidoglycan L,D-transpeptidase activity
B0005886cellular_componentplasma membrane
B0008360biological_processregulation of cell shape
B0009252biological_processpeptidoglycan biosynthetic process
B0016020cellular_componentmembrane
B0016740molecular_functiontransferase activity
B0016746molecular_functionacyltransferase activity
B0018104biological_processpeptidoglycan-protein cross-linking
B0046872molecular_functionmetal ion binding
B0071555biological_processcell wall organization
B0071972molecular_functionpeptidoglycan L,D-transpeptidase activity
Functional Information from PDB Data
site_idAC1
Number of Residues13
Detailsbinding site for residue 58U A 501
ChainResidue
AMET303
AASN356
AEDO516
AHOH606
AHOH625
ATYR318
AGLY332
AHIS336
ATRP340
ASER351
AHIS352
AGLY353
ACYS354

site_idAC2
Number of Residues8
Detailsbinding site for residue SO4 A 502
ChainResidue
AARG122
ASO4506
AHOH601
AHOH656
BPRO311
BVAL312
BASN313
BHOH641

site_idAC3
Number of Residues5
Detailsbinding site for residue SO4 A 503
ChainResidue
AARG371
AHOH626
AHOH652
AHOH695
AHOH758

site_idAC4
Number of Residues4
Detailsbinding site for residue SO4 A 504
ChainResidue
AMET157
ATYR330
AARG371
AHOH605

site_idAC5
Number of Residues5
Detailsbinding site for residue SO4 A 505
ChainResidue
ASER106
APRO107
AARG111
AHOH628
AHOH703

site_idAC6
Number of Residues6
Detailsbinding site for residue SO4 A 506
ChainResidue
AASN95
AARG99
ASO4502
AHOH601
AHOH619
BSER306

site_idAC7
Number of Residues3
Detailsbinding site for residue PEG A 507
ChainResidue
AASN204
AASN205
AHOH761

site_idAC8
Number of Residues4
Detailsbinding site for residue PEG A 508
ChainResidue
AGLY86
ALEU131
AGLY132
AHOH615

site_idAC9
Number of Residues8
Detailsbinding site for residue PEG A 509
ChainResidue
AGLU185
AALA199
APHE200
ATRP401
AARG402
AGLY404
APEG510
AHOH688

site_idAD1
Number of Residues7
Detailsbinding site for residue PEG A 510
ChainResidue
AILE188
ALYS189
AILE190
AGLY198
ATRP210
APEG509
AHOH750

site_idAD2
Number of Residues6
Detailsbinding site for residue PGE A 511
ChainResidue
AHIS214
APHE215
AGLU252
AILE254
AHOH638
BLYS186

site_idAD3
Number of Residues6
Detailsbinding site for residue PGE A 512
ChainResidue
ALYS189
AILE190
ATHR192
AVAL196
AHOH719
BASN260

site_idAD4
Number of Residues7
Detailsbinding site for residue GOL A 513
ChainResidue
AARG123
ATHR142
ASER358
APRO359
ASER360
AHOH603
AHOH714

site_idAD5
Number of Residues5
Detailsbinding site for residue GOL A 514
ChainResidue
AARG181
ATRP202
ALEU203
AHOH608
AHOH621

site_idAD6
Number of Residues6
Detailsbinding site for residue GOL A 515
ChainResidue
AVAL75
AALA77
APRO78
AGLN117
ALEU118
AHOH763

site_idAD7
Number of Residues5
Detailsbinding site for residue EDO A 516
ChainResidue
ATYR318
ASER331
AHIS352
AGLY353
A58U501

site_idAD8
Number of Residues4
Detailsbinding site for residue SO4 B 502
ChainResidue
BARG371
BHOH621
BHOH681
BARG297

site_idAD9
Number of Residues8
Detailsbinding site for residue SO4 B 503
ChainResidue
APRO311
AVAL312
AASN313
BARG122
BSO4504
BHOH616
BHOH623
BHOH749

site_idAE1
Number of Residues7
Detailsbinding site for residue SO4 B 504
ChainResidue
ASER306
APRO311
BASN95
BASN97
BARG99
BSO4503
BHOH658

site_idAE2
Number of Residues6
Detailsbinding site for residue SO4 B 505
ChainResidue
BARG104
BSER106
BPRO107
BARG111
BHOH630
BHOH748

site_idAE3
Number of Residues6
Detailsbinding site for residue PEG B 507
ChainResidue
ALEU62
AARG139
ALEU141
BASP399
BHOH609
BHOH622

site_idAE4
Number of Residues2
Detailsbinding site for residue PEG B 508
ChainResidue
BILE190
BTRP210

site_idAE5
Number of Residues4
Detailsbinding site for residue PEG B 509
ChainResidue
AVAL71
AHOH843
BGLU213
BHIS214

site_idAE6
Number of Residues6
Detailsbinding site for residue PEG B 510
ChainResidue
BPRO386
BGLY387
BGLN400
BPGE514
BHOH610
BHOH613

site_idAE7
Number of Residues4
Detailsbinding site for residue PEG B 511
ChainResidue
BASP251
BHIS368
BHOH611
BHOH635

site_idAE8
Number of Residues6
Detailsbinding site for residue PGE B 512
ChainResidue
BGLU376
BVAL378
BPRO397
BGOL515
BHOH603
BHOH763

site_idAE9
Number of Residues8
Detailsbinding site for residue PGE B 513
ChainResidue
BGLU168
BPRO169
BALA171
BGLY295
BSER296
BGLN327
BTYR330
BARG371

site_idAF1
Number of Residues8
Detailsbinding site for residue PGE B 514
ChainResidue
BARG181
BTYR201
BTRP202
BILE388
BASN405
BALA408
BPEG510
BHOH610

site_idAF2
Number of Residues6
Detailsbinding site for residue GOL B 515
ChainResidue
BGLU213
BHIS214
BPHE215
BILE291
BPGE512
BHOH750

site_idAF3
Number of Residues4
Detailsbinding site for residue GOL B 516
ChainResidue
BALA90
BVAL91
BLEU105
BTRP112

site_idAF4
Number of Residues4
Detailsbinding site for residue EDO B 517
ChainResidue
BTYR318
BSER331
BGLY332
B58U501

site_idAF5
Number of Residues15
Detailsbinding site for Di-peptide 58U B 501 and CYS B 354
ChainResidue
BSER279
BMET280
BMET303
BTYR318
BGLY332
BPHE334
BHIS336
BTRP340
BSER351
BHIS352
BGLY353
BLEU355
BASN356
BEDO517
BHOH612

site_idAF6
Number of Residues12
Detailsbinding site for Di-peptide SO4 B 506 and ARG B 123
ChainResidue
BASN95
BASP96
BARG122
BTYR124
BPHE143
BGLN144
BSER358
BSER358
BSER360
BHOH605
BHOH638
BHOH732

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues2
DetailsACT_SITE: Proton donor/acceptor => ECO:0000255|PROSITE-ProRule:PRU01373, ECO:0000305|PubMed:23519417
ChainResidueDetails
AHIS336
BHIS336

site_idSWS_FT_FI2
Number of Residues2
DetailsACT_SITE: Nucleophile => ECO:0000255|PROSITE-ProRule:PRU01373, ECO:0000269|PubMed:23519417
ChainResidueDetails
ACYS354
BCYS354

site_idSWS_FT_FI3
Number of Residues6
DetailsBINDING:
ChainResidueDetails
AASP232
AGLU235
AGLY236
BASP232
BGLU235
BGLY236

site_idSWS_FT_FI4
Number of Residues6
DetailsBINDING: BINDING => ECO:0000250
ChainResidueDetails
ATYR318
ASER331
AASN356
BTYR318
BSER331
BASN356

site_idSWS_FT_FI5
Number of Residues2
DetailsSITE: Binds to carbapenem drug (covalent)
ChainResidueDetails
ACYS354
BCYS354

237992

PDB entries from 2025-06-25

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