1RKD
E. COLI RIBOKINASE COMPLEXED WITH RIBOSE AND ADP
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0000166 | molecular_function | nucleotide binding |
| A | 0004747 | molecular_function | ribokinase activity |
| A | 0005524 | molecular_function | ATP binding |
| A | 0005737 | cellular_component | cytoplasm |
| A | 0005829 | cellular_component | cytosol |
| A | 0006014 | biological_process | D-ribose metabolic process |
| A | 0016301 | molecular_function | kinase activity |
| A | 0016740 | molecular_function | transferase activity |
| A | 0019303 | biological_process | D-ribose catabolic process |
| A | 0042803 | molecular_function | protein homodimerization activity |
| A | 0044281 | biological_process | small molecule metabolic process |
| A | 0046835 | biological_process | carbohydrate phosphorylation |
| A | 0046872 | molecular_function | metal ion binding |
Functional Information from PDB Data
| site_id | AB1 |
| Number of Residues | 4 |
| Details | RESIDUES MAKING DIRECT HYDROGEN BONDS WITH ADP. |
| Chain | Residue |
| A | ASN187 |
| A | THR223 |
| A | GLY225 |
| A | ALA280 |
| site_id | AB2 |
| Number of Residues | 7 |
| Details | RESIDUES MAKING WATER-MEDIATED HYDROGEN BONDS WITH ADP. |
| Chain | Residue |
| A | ASN166 |
| A | ASN187 |
| A | GLU190 |
| A | THR223 |
| A | PHE243 |
| A | VAL245 |
| A | ALA280 |
| site_id | AB3 |
| Number of Residues | 5 |
| Details | RESIDUES WITHIN VAN DER WAALS DISTANCE OF ADP. |
| Chain | Residue |
| A | GLY225 |
| A | VAL245 |
| A | ALA253 |
| A | ALA282 |
| A | VAL286 |
| site_id | RB1 |
| Number of Residues | 7 |
| Details | RESIDUES MAKING DIRECT HYDROGEN BONDS WITH RIBOSE. |
| Chain | Residue |
| A | ASN14 |
| A | ASP16 |
| A | GLY42 |
| A | LYS43 |
| A | ASN46 |
| A | GLU143 |
| A | ASP255 |
| site_id | RB2 |
| Number of Residues | 3 |
| Details | RESIDUES MAKING WATER-MEDIATED HYDROGEN BONDS WITH RIBOSE. |
| Chain | Residue |
| A | ASP255 |
| A | ALA252 |
| A | GLY254 |
| site_id | RB3 |
| Number of Residues | 5 |
| Details | RESIDUES WITHIN VAN DER WAALS DISTANCE OF RIBOSE. |
| Chain | Residue |
| A | ALA98 |
| A | ILE100 |
| A | ILE110 |
| A | ILE112 |
| A | ILE251 |
Functional Information from PROSITE/UniProt
| site_id | PS00584 |
| Number of Residues | 14 |
| Details | PFKB_KINASES_2 pfkB family of carbohydrate kinases signature 2. DTiAAGDtfnGALI |
| Chain | Residue | Details |
| A | ASP249-ILE262 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 1 |
| Details | Active site: {"description":"Proton acceptor","evidences":[{"source":"HAMAP-Rule","id":"MF_01987","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"11786021","evidenceCode":"ECO:0000305"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI2 |
| Number of Residues | 15 |
| Details | Binding site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_01987","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"10438599","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"11786021","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"9519409","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI3 |
| Number of Residues | 6 |
| Details | Binding site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_01987","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"11786021","evidenceCode":"ECO:0000305"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI4 |
| Number of Residues | 1 |
| Details | Binding site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_01987","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"10438599","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"11786021","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
Catalytic Information from CSA
| site_id | CSA1 |
| Number of Residues | 4 |
| Details | Annotated By Reference To The Literature 1rk2 |
| Chain | Residue | Details |
| A | GLY254 | |
| A | ASP255 | |
| A | ALA253 | |
| A | ALA252 |
| site_id | MCSA1 |
| Number of Residues | 4 |
| Details | M-CSA 663 |
| Chain | Residue | Details |
| A | ALA252 | electrostatic stabiliser, polar interaction |
| A | ALA253 | electrostatic stabiliser, polar interaction |
| A | GLY254 | electrostatic stabiliser, polar interaction |
| A | ASP255 | electrostatic stabiliser, proton acceptor, proton donor |
