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1KEP

The crystal structure of dTDP-D-glucose 4,6-dehydratase (RmlB) from Streptococcus suis with dTDP-xylose bound

Functional Information from GO Data
ChainGOidnamespacecontents
A0000166molecular_functionnucleotide binding
A0008460molecular_functiondTDP-glucose 4,6-dehydratase activity
A0009225biological_processnucleotide-sugar metabolic process
A0016829molecular_functionlyase activity
B0000166molecular_functionnucleotide binding
B0008460molecular_functiondTDP-glucose 4,6-dehydratase activity
B0009225biological_processnucleotide-sugar metabolic process
B0016829molecular_functionlyase activity
Functional Information from PDB Data
site_idAC1
Number of Residues8
DetailsBINDING SITE FOR RESIDUE SO4 A 6001
ChainResidue
AGLY53
AASP54
AARG55
AHOH6069
AHOH6132
AHOH6200
AHOH6203
AHOH6406

site_idAC2
Number of Residues8
DetailsBINDING SITE FOR RESIDUE SO4 A 6002
ChainResidue
ATHR309
AASP310
APHE311
ASER312
AHOH6163
AHOH6188
AHOH6202
ALYS258

site_idAC3
Number of Residues7
DetailsBINDING SITE FOR RESIDUE SO4 B 6003
ChainResidue
BLYS258
BTHR309
BASP310
BPHE311
BSER312
BHOH6143
BHOH6263

site_idAC4
Number of Residues36
DetailsBINDING SITE FOR RESIDUE NAD A 1400
ChainResidue
AALA13
AGLY14
APHE15
AILE16
AASP37
ALYS38
ALEU39
ATHR40
AALA42
AGLY43
AGLY61
AASP62
AILE63
ATYR82
AALA83
AALA84
ASER86
ATHR101
AVAL123
ASER124
ATYR161
ALYS165
ACYS188
ASER189
AASN190
AASN191
ATDX3500
AHOH6003
AHOH6005
AHOH6006
AHOH6007
AHOH6017
AHOH6026
AHOH6033
AHOH6038
AHOH6039

site_idAC5
Number of Residues35
DetailsBINDING SITE FOR RESIDUE NAD B 2400
ChainResidue
BALA13
BGLY14
BPHE15
BILE16
BASP37
BLYS38
BLEU39
BTHR40
BALA42
BGLY43
BGLY61
BASP62
BILE63
BTYR82
BALA83
BALA84
BSER86
BTHR101
BVAL123
BSER124
BTYR161
BLYS165
BCYS188
BASN190
BASN191
BTDX4500
BHOH6005
BHOH6014
BHOH6017
BHOH6019
BHOH6021
BHOH6025
BHOH6027
BHOH6028
BHOH6046

site_idAC6
Number of Residues13
DetailsBINDING SITE FOR RESIDUE TDX A 3500
ChainResidue
AASN190
ALYS200
AARG225
AARG284
ANAD1400
AHOH6011
AHOH6028
AHOH6121
ASER86
AASN88
ATHR125
AGLU127
ATYR161

site_idAC7
Number of Residues24
DetailsBINDING SITE FOR RESIDUE TDX B 4500
ChainResidue
BSER86
BHIS87
BASN88
BTHR125
BGLU127
BTYR161
BASN190
BGLU199
BLYS200
BPHE201
BARG204
BGLN205
BLYS216
BTYR218
BARG225
BASN260
BARG284
BHIS287
BTYR340
BNAD2400
BHOH6023
BHOH6036
BHOH6040
BHOH6131

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues2
DetailsACT_SITE: Proton donor => ECO:0000250|UniProtKB:P27830
ChainResidueDetails
AASP126
BASP126

site_idSWS_FT_FI2
Number of Residues2
DetailsACT_SITE: Proton acceptor => ECO:0000250|UniProtKB:P27830
ChainResidueDetails
AGLU127
BGLU127

site_idSWS_FT_FI3
Number of Residues2
DetailsACT_SITE: Proton acceptor => ECO:0000305|PubMed:11796113, ECO:0007744|PDB:1KEP, ECO:0007744|PDB:1KET
ChainResidueDetails
ATYR161
BTYR161

site_idSWS_FT_FI4
Number of Residues14
DetailsBINDING: BINDING => ECO:0000269|PubMed:11796113, ECO:0007744|PDB:1KEP, ECO:0007744|PDB:1KET
ChainResidueDetails
APHE15
BASP62
BTYR82
BTHR101
BASN191
BLYS200
AASP37
AASP62
ATYR82
ATHR101
AASN191
ALYS200
BPHE15
BASP37

site_idSWS_FT_FI5
Number of Residues2
DetailsBINDING: BINDING => ECO:0000250|UniProtKB:P26391
ChainResidueDetails
ASER86
BSER86

site_idSWS_FT_FI6
Number of Residues10
DetailsBINDING: BINDING => ECO:0000269|PubMed:11796113, ECO:0007744|PDB:1KET
ChainResidueDetails
AASN88
BASN260
AASN190
ALYS216
AARG225
AASN260
BASN88
BASN190
BLYS216
BARG225

site_idSWS_FT_FI7
Number of Residues2
DetailsBINDING: BINDING => ECO:0000269|PubMed:11796113, ECO:0007744|PDB:1KEP
ChainResidueDetails
ATHR125
BTHR125

site_idSWS_FT_FI8
Number of Residues2
DetailsBINDING: BINDING => ECO:0000305|PubMed:11796113, ECO:0007744|PDB:1KEP, ECO:0007744|PDB:1KET
ChainResidueDetails
ATYR161
BTYR161

site_idSWS_FT_FI9
Number of Residues2
DetailsBINDING: BINDING => ECO:0000305|PubMed:11796113, ECO:0007744|PDB:1KET
ChainResidueDetails
AASP283
BASP283

Catalytic Information from CSA
site_idCSA1
Number of Residues3
DetailsAnnotated By Reference To The Literature 1db3
ChainResidueDetails
ATYR161
ALYS165
ATHR125

site_idCSA2
Number of Residues3
DetailsAnnotated By Reference To The Literature 1db3
ChainResidueDetails
BTYR161
BLYS165
BTHR125

site_idCSA3
Number of Residues4
DetailsAnnotated By Reference To The Literature 1db3
ChainResidueDetails
ATYR161
AGLU127
ATHR125
ALYS165

site_idCSA4
Number of Residues4
DetailsAnnotated By Reference To The Literature 1db3
ChainResidueDetails
BTYR161
BGLU127
BTHR125
BLYS165

site_idCSA5
Number of Residues2
DetailsAnnotated By Reference To The Literature 1db3
ChainResidueDetails
ATYR161
ALYS165

site_idCSA6
Number of Residues2
DetailsAnnotated By Reference To The Literature 1db3
ChainResidueDetails
BTYR161
BLYS165

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PDB entries from 2024-07-17

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