1KEP
The crystal structure of dTDP-D-glucose 4,6-dehydratase (RmlB) from Streptococcus suis with dTDP-xylose bound
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0000166 | molecular_function | nucleotide binding |
| A | 0008460 | molecular_function | dTDP-glucose 4,6-dehydratase activity |
| A | 0009225 | biological_process | nucleotide-sugar metabolic process |
| A | 0016829 | molecular_function | lyase activity |
| B | 0000166 | molecular_function | nucleotide binding |
| B | 0008460 | molecular_function | dTDP-glucose 4,6-dehydratase activity |
| B | 0009225 | biological_process | nucleotide-sugar metabolic process |
| B | 0016829 | molecular_function | lyase activity |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 8 |
| Details | BINDING SITE FOR RESIDUE SO4 A 6001 |
| Chain | Residue |
| A | GLY53 |
| A | ASP54 |
| A | ARG55 |
| A | HOH6069 |
| A | HOH6132 |
| A | HOH6200 |
| A | HOH6203 |
| A | HOH6406 |
| site_id | AC2 |
| Number of Residues | 8 |
| Details | BINDING SITE FOR RESIDUE SO4 A 6002 |
| Chain | Residue |
| A | THR309 |
| A | ASP310 |
| A | PHE311 |
| A | SER312 |
| A | HOH6163 |
| A | HOH6188 |
| A | HOH6202 |
| A | LYS258 |
| site_id | AC3 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE SO4 B 6003 |
| Chain | Residue |
| B | LYS258 |
| B | THR309 |
| B | ASP310 |
| B | PHE311 |
| B | SER312 |
| B | HOH6143 |
| B | HOH6263 |
| site_id | AC4 |
| Number of Residues | 36 |
| Details | BINDING SITE FOR RESIDUE NAD A 1400 |
| Chain | Residue |
| A | ALA13 |
| A | GLY14 |
| A | PHE15 |
| A | ILE16 |
| A | ASP37 |
| A | LYS38 |
| A | LEU39 |
| A | THR40 |
| A | ALA42 |
| A | GLY43 |
| A | GLY61 |
| A | ASP62 |
| A | ILE63 |
| A | TYR82 |
| A | ALA83 |
| A | ALA84 |
| A | SER86 |
| A | THR101 |
| A | VAL123 |
| A | SER124 |
| A | TYR161 |
| A | LYS165 |
| A | CYS188 |
| A | SER189 |
| A | ASN190 |
| A | ASN191 |
| A | TDX3500 |
| A | HOH6003 |
| A | HOH6005 |
| A | HOH6006 |
| A | HOH6007 |
| A | HOH6017 |
| A | HOH6026 |
| A | HOH6033 |
| A | HOH6038 |
| A | HOH6039 |
| site_id | AC5 |
| Number of Residues | 35 |
| Details | BINDING SITE FOR RESIDUE NAD B 2400 |
| Chain | Residue |
| B | ALA13 |
| B | GLY14 |
| B | PHE15 |
| B | ILE16 |
| B | ASP37 |
| B | LYS38 |
| B | LEU39 |
| B | THR40 |
| B | ALA42 |
| B | GLY43 |
| B | GLY61 |
| B | ASP62 |
| B | ILE63 |
| B | TYR82 |
| B | ALA83 |
| B | ALA84 |
| B | SER86 |
| B | THR101 |
| B | VAL123 |
| B | SER124 |
| B | TYR161 |
| B | LYS165 |
| B | CYS188 |
| B | ASN190 |
| B | ASN191 |
| B | TDX4500 |
| B | HOH6005 |
| B | HOH6014 |
| B | HOH6017 |
| B | HOH6019 |
| B | HOH6021 |
| B | HOH6025 |
| B | HOH6027 |
| B | HOH6028 |
| B | HOH6046 |
| site_id | AC6 |
| Number of Residues | 13 |
| Details | BINDING SITE FOR RESIDUE TDX A 3500 |
| Chain | Residue |
| A | ASN190 |
| A | LYS200 |
| A | ARG225 |
| A | ARG284 |
| A | NAD1400 |
| A | HOH6011 |
| A | HOH6028 |
| A | HOH6121 |
| A | SER86 |
| A | ASN88 |
| A | THR125 |
| A | GLU127 |
| A | TYR161 |
| site_id | AC7 |
| Number of Residues | 24 |
| Details | BINDING SITE FOR RESIDUE TDX B 4500 |
| Chain | Residue |
| B | SER86 |
| B | HIS87 |
| B | ASN88 |
| B | THR125 |
| B | GLU127 |
| B | TYR161 |
| B | ASN190 |
| B | GLU199 |
| B | LYS200 |
| B | PHE201 |
| B | ARG204 |
| B | GLN205 |
| B | LYS216 |
| B | TYR218 |
| B | ARG225 |
| B | ASN260 |
| B | ARG284 |
| B | HIS287 |
| B | TYR340 |
| B | NAD2400 |
| B | HOH6023 |
| B | HOH6036 |
| B | HOH6040 |
| B | HOH6131 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 2 |
| Details | Active site: {"description":"Proton donor","evidences":[{"source":"UniProtKB","id":"P27830","evidenceCode":"ECO:0000250"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI2 |
| Number of Residues | 2 |
| Details | Active site: {"description":"Proton acceptor","evidences":[{"source":"UniProtKB","id":"P27830","evidenceCode":"ECO:0000250"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI3 |
| Number of Residues | 2 |
| Details | Active site: {"description":"Proton acceptor","evidences":[{"source":"PubMed","id":"11796113","evidenceCode":"ECO:0000305"},{"source":"PDB","id":"1KEP","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1KET","evidenceCode":"ECO:0007744"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI4 |
| Number of Residues | 28 |
| Details | Binding site: {"evidences":[{"source":"PubMed","id":"11796113","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1KEP","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1KET","evidenceCode":"ECO:0007744"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI6 |
| Number of Residues | 12 |
| Details | Binding site: {"evidences":[{"source":"PubMed","id":"11796113","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1KET","evidenceCode":"ECO:0007744"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI8 |
| Number of Residues | 2 |
| Details | Binding site: {"evidences":[{"source":"PubMed","id":"11796113","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1KEP","evidenceCode":"ECO:0007744"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI9 |
| Number of Residues | 8 |
| Details | Binding site: {"evidences":[{"source":"PubMed","id":"11796113","evidenceCode":"ECO:0000305"},{"source":"PDB","id":"1KEP","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1KET","evidenceCode":"ECO:0007744"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI10 |
| Number of Residues | 8 |
| Details | Binding site: {"evidences":[{"source":"PubMed","id":"11796113","evidenceCode":"ECO:0000305"},{"source":"PDB","id":"1KET","evidenceCode":"ECO:0007744"}]} |
| Chain | Residue | Details |
Catalytic Information from CSA
| site_id | CSA1 |
| Number of Residues | 3 |
| Details | Annotated By Reference To The Literature 1db3 |
| Chain | Residue | Details |
| A | TYR161 | |
| A | LYS165 | |
| A | THR125 |
| site_id | CSA2 |
| Number of Residues | 3 |
| Details | Annotated By Reference To The Literature 1db3 |
| Chain | Residue | Details |
| B | TYR161 | |
| B | LYS165 | |
| B | THR125 |
| site_id | CSA3 |
| Number of Residues | 4 |
| Details | Annotated By Reference To The Literature 1db3 |
| Chain | Residue | Details |
| A | TYR161 | |
| A | GLU127 | |
| A | THR125 | |
| A | LYS165 |
| site_id | CSA4 |
| Number of Residues | 4 |
| Details | Annotated By Reference To The Literature 1db3 |
| Chain | Residue | Details |
| B | TYR161 | |
| B | GLU127 | |
| B | THR125 | |
| B | LYS165 |
| site_id | CSA5 |
| Number of Residues | 2 |
| Details | Annotated By Reference To The Literature 1db3 |
| Chain | Residue | Details |
| A | TYR161 | |
| A | LYS165 |
| site_id | CSA6 |
| Number of Residues | 2 |
| Details | Annotated By Reference To The Literature 1db3 |
| Chain | Residue | Details |
| B | TYR161 | |
| B | LYS165 |
