5C41
Crystal structure of human ribokinase in complex with AMPPCP in P21 spacegroup and with 4 protomers
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| 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 | 0006753 | biological_process | nucleoside phosphate metabolic process |
| A | 0016301 | molecular_function | kinase activity |
| A | 0016310 | biological_process | phosphorylation |
| 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 | 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 | 0006753 | biological_process | nucleoside phosphate metabolic process |
| B | 0016301 | molecular_function | kinase activity |
| B | 0016310 | biological_process | phosphorylation |
| 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 |
| C | 0004747 | molecular_function | ribokinase activity |
| C | 0005515 | molecular_function | protein binding |
| C | 0005524 | molecular_function | ATP binding |
| C | 0005634 | cellular_component | nucleus |
| C | 0005737 | cellular_component | cytoplasm |
| C | 0005829 | cellular_component | cytosol |
| C | 0006014 | biological_process | D-ribose metabolic process |
| C | 0006098 | biological_process | pentose-phosphate shunt |
| C | 0006753 | biological_process | nucleoside phosphate metabolic process |
| C | 0016301 | molecular_function | kinase activity |
| C | 0016310 | biological_process | phosphorylation |
| C | 0019303 | biological_process | D-ribose catabolic process |
| C | 0042802 | molecular_function | identical protein binding |
| C | 0046835 | biological_process | carbohydrate phosphorylation |
| C | 0046872 | molecular_function | metal ion binding |
| D | 0004747 | molecular_function | ribokinase activity |
| D | 0005515 | molecular_function | protein binding |
| D | 0005524 | molecular_function | ATP binding |
| D | 0005634 | cellular_component | nucleus |
| D | 0005737 | cellular_component | cytoplasm |
| D | 0005829 | cellular_component | cytosol |
| D | 0006014 | biological_process | D-ribose metabolic process |
| D | 0006098 | biological_process | pentose-phosphate shunt |
| D | 0006753 | biological_process | nucleoside phosphate metabolic process |
| D | 0016301 | molecular_function | kinase activity |
| D | 0016310 | biological_process | phosphorylation |
| D | 0019303 | biological_process | D-ribose catabolic process |
| D | 0042802 | molecular_function | identical protein binding |
| D | 0046835 | biological_process | carbohydrate phosphorylation |
| D | 0046872 | molecular_function | metal ion binding |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 27 |
| Details | binding site for residue ACP A 401 |
| Chain | Residue |
| A | ASN199 |
| A | GLY268 |
| A | ASN295 |
| A | ALA298 |
| A | ALA299 |
| A | NA403 |
| A | HOH501 |
| A | HOH507 |
| A | HOH515 |
| A | HOH525 |
| A | HOH530 |
| A | THR235 |
| A | HOH560 |
| A | HOH576 |
| A | HOH596 |
| A | HOH615 |
| A | HOH621 |
| A | HOH684 |
| A | HOH686 |
| A | HOH688 |
| A | LEU236 |
| A | GLY237 |
| A | ALA238 |
| A | GLY240 |
| A | VAL259 |
| A | THR264 |
| A | ALA267 |
| 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 | HOH579 |
| A | HOH629 |
| site_id | AC3 |
| Number of Residues | 7 |
| Details | binding site for residue NA A 403 |
| Chain | Residue |
| A | ACP401 |
| A | HOH501 |
| A | HOH513 |
| A | HOH530 |
| A | HOH569 |
| A | HOH615 |
| A | HOH655 |
| site_id | AC4 |
| Number of Residues | 28 |
| Details | binding site for residue ACP B 401 |
| Chain | Residue |
| B | ASN199 |
| B | THR235 |
| B | GLY237 |
| B | ALA238 |
| B | GLY240 |
| B | THR256 |
| B | GLU257 |
| B | VAL259 |
| B | THR264 |
| B | THR265 |
| B | GLY266 |
| B | ALA267 |
| B | GLY268 |
| B | ASN295 |
| B | ALA298 |
| B | ALA299 |
| B | HOH510 |
| B | HOH542 |
| B | HOH543 |
| B | HOH548 |
| B | HOH572 |
| B | HOH573 |
| B | HOH577 |
| B | HOH637 |
| B | HOH644 |
| B | HOH659 |
| B | HOH663 |
| B | HOH671 |
| site_id | AC5 |
| Number of Residues | 6 |
| Details | binding site for residue NA B 402 |
| Chain | Residue |
| B | ASP263 |
| B | SER301 |
| B | ALA304 |
| B | GLY306 |
| B | SER310 |
| B | HOH624 |
| site_id | AC6 |
| Number of Residues | 6 |
| Details | binding site for residue NA B 403 |
| Chain | Residue |
| B | HOH523 |
| B | HOH536 |
| B | HOH542 |
| B | HOH612 |
| B | HOH641 |
| B | HOH663 |
| site_id | AC7 |
| Number of Residues | 25 |
| Details | binding site for residue ACP C 401 |
| Chain | Residue |
| C | HOH556 |
| C | HOH578 |
| C | HOH583 |
| C | HOH593 |
| C | HOH610 |
| C | HOH628 |
| C | ASN199 |
| C | THR235 |
| C | LEU236 |
| C | GLY237 |
| C | ALA238 |
| C | GLY240 |
| C | VAL259 |
| C | ALA267 |
| C | GLY268 |
| C | ASN295 |
| C | ALA298 |
| C | ALA299 |
| C | NA403 |
| C | HOH504 |
| C | HOH508 |
| C | HOH520 |
| C | HOH537 |
| C | HOH538 |
| C | HOH550 |
| site_id | AC8 |
| Number of Residues | 7 |
| Details | binding site for residue NA C 402 |
| Chain | Residue |
| C | ASP263 |
| C | SER301 |
| C | ALA304 |
| C | GLY306 |
| C | SER310 |
| C | HOH502 |
| C | HOH629 |
| site_id | AC9 |
| Number of Residues | 6 |
| Details | binding site for residue NA C 403 |
| Chain | Residue |
| C | ACP401 |
| C | HOH519 |
| C | HOH520 |
| C | HOH574 |
| C | HOH685 |
| C | HOH710 |
| site_id | AD1 |
| Number of Residues | 17 |
| Details | binding site for residue ACP D 401 |
| Chain | Residue |
| D | ASN199 |
| D | THR235 |
| D | GLY237 |
| D | ALA238 |
| D | GLY240 |
| D | VAL259 |
| D | THR264 |
| D | ALA267 |
| D | GLY268 |
| D | ASN295 |
| D | ALA298 |
| D | ALA299 |
| D | HOH510 |
| D | HOH516 |
| D | HOH524 |
| D | HOH577 |
| D | HOH585 |
| site_id | AD2 |
| Number of Residues | 5 |
| Details | binding site for residue PO4 D 402 |
| Chain | Residue |
| D | TYR282 |
| D | PRO283 |
| D | ASN284 |
| D | LEU285 |
| D | HOH547 |
| site_id | AD3 |
| Number of Residues | 6 |
| Details | binding site for residue NA D 403 |
| Chain | Residue |
| D | ASP263 |
| D | SER301 |
| D | ALA304 |
| D | SER310 |
| D | HOH581 |
| D | HOH594 |
| site_id | AD4 |
| Number of Residues | 6 |
| Details | binding site for residue NA D 404 |
| Chain | Residue |
| D | HOH511 |
| D | HOH521 |
| D | HOH524 |
| D | HOH552 |
| D | HOH577 |
| D | HOH611 |
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 | 4 |
| Details | ACT_SITE: Proton acceptor => ECO:0000250|UniProtKB:P0A9J6, ECO:0000255|HAMAP-Rule:MF_03215 |
| Chain | Residue | Details |
| A | ASP269 | |
| B | ASP269 | |
| C | ASP269 | |
| D | ASP269 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 24 |
| Details | BINDING: BINDING => ECO:0000250|UniProtKB:P0A9J6, ECO:0000255|HAMAP-Rule:MF_03215 |
| Chain | Residue | Details |
| A | MET25 | |
| B | THR265 | |
| B | ASP269 | |
| B | GLY306 | |
| C | MET25 | |
| C | GLY53 | |
| C | GLU154 | |
| C | THR265 | |
| C | ASP269 | |
| C | GLY306 | |
| D | MET25 | |
| A | GLY53 | |
| D | GLY53 | |
| D | GLU154 | |
| D | THR265 | |
| D | ASP269 | |
| D | GLY306 | |
| A | GLU154 | |
| A | THR265 | |
| A | ASP269 | |
| A | GLY306 | |
| B | MET25 | |
| B | GLY53 | |
| B | GLU154 |
| site_id | SWS_FT_FI3 |
| Number of Residues | 20 |
| Details | BINDING: BINDING => ECO:0000255|HAMAP-Rule:MF_03215, ECO:0000269|Ref.7 |
| Chain | Residue | Details |
| A | ASN199 | |
| B | ASN295 | |
| C | ASN199 | |
| C | THR235 | |
| C | THR256 | |
| C | GLY268 | |
| C | ASN295 | |
| D | ASN199 | |
| D | THR235 | |
| D | THR256 | |
| D | GLY268 | |
| A | THR235 | |
| D | ASN295 | |
| A | THR256 | |
| A | GLY268 | |
| A | ASN295 | |
| B | ASN199 | |
| B | THR235 | |
| B | THR256 | |
| B | GLY268 |
| site_id | SWS_FT_FI4 |
| Number of Residues | 16 |
| Details | BINDING: BINDING => ECO:0000255|HAMAP-Rule:MF_03215, ECO:0000305|Ref.7 |
| Chain | Residue | Details |
| A | ASP263 | |
| C | SER301 | |
| C | ALA304 | |
| C | SER310 | |
| D | ASP263 | |
| D | SER301 | |
| D | ALA304 | |
| D | SER310 | |
| A | SER301 | |
| A | ALA304 | |
| A | SER310 | |
| B | ASP263 | |
| B | SER301 | |
| B | ALA304 | |
| B | SER310 | |
| C | ASP263 |
