5C40
Crystal structure of human ribokinase in complex with AMPPCP in P21 spacegroup
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0000166 | molecular_function | nucleotide binding |
| A | 0004747 | molecular_function | ribokinase activity |
| A | 0005515 | molecular_function | protein binding |
| A | 0005524 | molecular_function | ATP binding |
| A | 0005634 | cellular_component | nucleus |
| A | 0005737 | cellular_component | cytoplasm |
| A | 0005829 | cellular_component | cytosol |
| A | 0006014 | biological_process | D-ribose metabolic process |
| A | 0006098 | biological_process | pentose-phosphate shunt |
| A | 0016301 | molecular_function | kinase activity |
| A | 0016740 | molecular_function | transferase activity |
| A | 0019303 | biological_process | D-ribose catabolic process |
| A | 0042802 | molecular_function | identical protein binding |
| A | 0046835 | biological_process | carbohydrate phosphorylation |
| A | 0046872 | molecular_function | metal ion binding |
| B | 0000166 | molecular_function | nucleotide binding |
| B | 0004747 | molecular_function | ribokinase activity |
| B | 0005515 | molecular_function | protein binding |
| B | 0005524 | molecular_function | ATP binding |
| B | 0005634 | cellular_component | nucleus |
| B | 0005737 | cellular_component | cytoplasm |
| B | 0005829 | cellular_component | cytosol |
| B | 0006014 | biological_process | D-ribose metabolic process |
| B | 0006098 | biological_process | pentose-phosphate shunt |
| B | 0016301 | molecular_function | kinase activity |
| B | 0016740 | molecular_function | transferase activity |
| B | 0019303 | biological_process | D-ribose catabolic process |
| B | 0042802 | molecular_function | identical protein binding |
| B | 0046835 | biological_process | carbohydrate phosphorylation |
| B | 0046872 | molecular_function | metal ion binding |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 26 |
| Details | binding site for residue ACP A 401 |
| Chain | Residue |
| A | ASN199 |
| A | ALA267 |
| A | GLY268 |
| A | ASN295 |
| A | ALA298 |
| A | ALA299 |
| A | HOH501 |
| A | HOH503 |
| A | HOH504 |
| A | HOH513 |
| A | HOH542 |
| A | THR235 |
| A | HOH562 |
| A | HOH575 |
| A | HOH587 |
| A | HOH647 |
| A | HOH672 |
| A | HOH694 |
| A | HOH751 |
| A | GLY237 |
| A | ALA238 |
| A | GLY240 |
| A | THR256 |
| A | THR264 |
| A | THR265 |
| A | GLY266 |
| site_id | AC2 |
| Number of Residues | 6 |
| Details | binding site for residue NA A 402 |
| Chain | Residue |
| A | ASP263 |
| A | SER301 |
| A | ALA304 |
| A | SER310 |
| A | HOH608 |
| A | HOH660 |
| site_id | AC3 |
| Number of Residues | 6 |
| Details | binding site for residue NA A 403 |
| Chain | Residue |
| A | HOH538 |
| A | HOH575 |
| A | HOH580 |
| A | HOH587 |
| A | HOH614 |
| A | HOH688 |
| site_id | AC4 |
| Number of Residues | 6 |
| Details | binding site for residue PO4 A 404 |
| Chain | Residue |
| A | HIS325 |
| A | HIS327 |
| A | HIS328 |
| A | HOH511 |
| A | HOH512 |
| A | HOH567 |
| site_id | AC5 |
| Number of Residues | 23 |
| Details | binding site for residue ACP B 401 |
| Chain | Residue |
| B | ASN199 |
| B | THR235 |
| B | GLY237 |
| B | ALA238 |
| B | GLY240 |
| B | VAL259 |
| B | THR264 |
| B | ALA267 |
| B | GLY268 |
| B | ASN295 |
| B | ALA298 |
| B | ALA299 |
| B | HOH509 |
| B | HOH535 |
| B | HOH560 |
| B | HOH577 |
| B | HOH601 |
| B | HOH620 |
| B | HOH640 |
| B | HOH649 |
| B | HOH655 |
| B | HOH667 |
| B | HOH682 |
| site_id | AC6 |
| Number of Residues | 7 |
| Details | binding site for residue NA B 402 |
| Chain | Residue |
| B | ASP263 |
| B | THR265 |
| B | SER301 |
| B | ALA304 |
| B | GLY306 |
| B | SER310 |
| B | HOH638 |
| site_id | AC7 |
| Number of Residues | 6 |
| Details | binding site for residue NA B 403 |
| Chain | Residue |
| B | HOH512 |
| B | HOH533 |
| B | HOH535 |
| B | HOH587 |
| B | HOH666 |
| B | HOH682 |
| site_id | AC8 |
| Number of Residues | 3 |
| Details | binding site for residue PO4 B 404 |
| Chain | Residue |
| B | LEU323 |
| B | GLU324 |
| B | HIS325 |
| site_id | AC9 |
| Number of Residues | 1 |
| Details | binding site for residue PO4 B 405 |
| Chain | Residue |
| B | HIS43 |
Functional Information from PROSITE/UniProt
| site_id | PS00584 |
| Number of Residues | 14 |
| Details | PFKB_KINASES_2 pfkB family of carbohydrate kinases signature 2. DTtGAGDsfvGALA |
| Chain | Residue | Details |
| A | ASP263-ALA276 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 2 |
| Details | Active site: {"description":"Proton acceptor","evidences":[{"source":"UniProtKB","id":"P0A9J6","evidenceCode":"ECO:0000250"},{"source":"HAMAP-Rule","id":"MF_03215","evidenceCode":"ECO:0000255"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI2 |
| Number of Residues | 20 |
| Details | Binding site: {"evidences":[{"source":"UniProtKB","id":"P0A9J6","evidenceCode":"ECO:0000250"},{"source":"HAMAP-Rule","id":"MF_03215","evidenceCode":"ECO:0000255"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI3 |
| Number of Residues | 18 |
| Details | Binding site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_03215","evidenceCode":"ECO:0000255"},{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"submission","publicationDate":"JAN-2006","submissionDatabase":"PDB data bank","title":"Crystal structure of human ribokinase.","authoringGroup":["Structural genomics consortium (SGC)"]}}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI4 |
| Number of Residues | 8 |
| Details | Binding site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_03215","evidenceCode":"ECO:0000255"},{"source":"Reference","evidenceCode":"ECO:0000305","citation":{"citationType":"submission","publicationDate":"JAN-2006","submissionDatabase":"PDB data bank","title":"Crystal structure of human ribokinase.","authoringGroup":["Structural genomics consortium (SGC)"]}}]} |
| Chain | Residue | Details |
