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 |