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1KC1

Crystal structure of dTDP-6-deoxy-L-lyxo-4-hexulose reductase (RmlD) in complex with NADPH

Functional Information from GO Data
ChainGOidnamespacecontents
A0005829cellular_componentcytosol
A0008831molecular_functiondTDP-4-dehydrorhamnose reductase activity
A0009058biological_processbiosynthetic process
A0009103biological_processlipopolysaccharide biosynthetic process
A0009243biological_processO antigen biosynthetic process
A0016491molecular_functionoxidoreductase activity
A0019305biological_processdTDP-rhamnose biosynthetic process
A0045226biological_processextracellular polysaccharide biosynthetic process
A0046872molecular_functionmetal ion binding
Functional Information from PDB Data
site_idAC1
Number of Residues7
DetailsBINDING SITE FOR RESIDUE MG A 501
ChainResidue
AGLU190
AHOH923
AHOH923
AHOH936
AHOH936
AHOH937
AHOH937

site_idAC2
Number of Residues2
DetailsBINDING SITE FOR RESIDUE SO4 A 601
ChainResidue
ALYS158
ATHR295

site_idAC3
Number of Residues22
DetailsBINDING SITE FOR RESIDUE NDP A 901
ChainResidue
AGLY10
AGLN11
AVAL12
AVAL31
AGLY38
AASP39
APHE40
AALA61
AALA62
AALA63
ATHR65
ATYR102
ASER103
ATYR128
ALYS132
ATHR151
AVAL154
AGLN174
AHOH938
AHOH939
AHOH952
AHOH957

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues1
DetailsACT_SITE: Proton donor/acceptor => ECO:0000269|PubMed:12057193
ChainResidueDetails
ATYR128

site_idSWS_FT_FI2
Number of Residues2
DetailsBINDING: BINDING => ECO:0000269|PubMed:12057193, ECO:0007744|PDB:1N2S
ChainResidueDetails
AGLY10
AASP30

site_idSWS_FT_FI3
Number of Residues6
DetailsBINDING: BINDING => ECO:0000269|PubMed:12057193, ECO:0007744|PDB:1KC1
ChainResidueDetails
AGLN11
AASP39
AALA63
ATYR102
ATYR128
ALYS132

site_idSWS_FT_FI4
Number of Residues2
DetailsBINDING: BINDING => ECO:0000269|PubMed:12057193, ECO:0007744|PDB:1KC3
ChainResidueDetails
ATHR104
ATRP153

site_idSWS_FT_FI5
Number of Residues1
DetailsSITE: Could provide a fine-tuning to achieve optimal pKa matching between active site and substrate => ECO:0000305|PubMed:12057193
ChainResidueDetails
ATHR104

Catalytic Information from CSA
site_idCSA1
Number of Residues4
DetailsAnnotated By Reference To The Literature 1db3
ChainResidueDetails
ATHR104
ATYR106
ATYR128
ALYS132

site_idCSA2
Number of Residues3
DetailsAnnotated By Reference To The Literature 1db3
ChainResidueDetails
ATHR104
ALYS132
ATYR128

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PDB entries from 2024-11-06

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