5BYF
Crystal structure of human ribokinase in complex with AMP
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 | 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 | 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 | 15 |
Details | binding site for residue AMP A 401 |
Chain | Residue |
A | ASN199 |
A | HOH515 |
A | HOH516 |
A | HOH548 |
A | HOH593 |
A | HOH595 |
A | HOH637 |
A | THR235 |
A | GLY237 |
A | ALA238 |
A | GLY240 |
A | ALA267 |
A | ASN295 |
A | ALA298 |
A | HOH507 |
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 | HOH528 |
A | HOH550 |
site_id | AC3 |
Number of Residues | 5 |
Details | binding site for residue NA A 403 |
Chain | Residue |
A | HOH517 |
A | HOH539 |
A | HOH558 |
A | HOH593 |
A | HOH613 |
site_id | AC4 |
Number of Residues | 10 |
Details | binding site for residue AMP B 401 |
Chain | Residue |
B | ASN199 |
B | THR235 |
B | GLY237 |
B | ALA238 |
B | GLY240 |
B | ALA267 |
B | GLY268 |
B | ASN295 |
B | ALA298 |
B | HOH538 |
site_id | AC5 |
Number of Residues | 6 |
Details | binding site for residue NA B 402 |
Chain | Residue |
B | ASP263 |
B | SER301 |
B | ALA304 |
B | SER310 |
B | HOH541 |
B | HOH567 |
site_id | AC6 |
Number of Residues | 5 |
Details | binding site for residue NA B 403 |
Chain | Residue |
B | HOH508 |
B | HOH514 |
B | HOH529 |
B | HOH609 |
B | HOH611 |
site_id | AC7 |
Number of Residues | 2 |
Details | binding site for residue CL B 404 |
Chain | Residue |
A | ARG169 |
B | ARG34 |
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 | ACT_SITE: Proton acceptor => ECO:0000250|UniProtKB:P0A9J6, ECO:0000255|HAMAP-Rule:MF_03215 |
Chain | Residue | Details |
A | ASP269 | |
B | ASP269 |
site_id | SWS_FT_FI2 |
Number of Residues | 12 |
Details | BINDING: BINDING => ECO:0000250|UniProtKB:P0A9J6, ECO:0000255|HAMAP-Rule:MF_03215 |
Chain | Residue | Details |
A | MET25 | |
B | THR265 | |
B | ASP269 | |
B | GLY306 | |
A | GLY53 | |
A | GLU154 | |
A | THR265 | |
A | ASP269 | |
A | GLY306 | |
B | MET25 | |
B | GLY53 | |
B | GLU154 |
site_id | SWS_FT_FI3 |
Number of Residues | 10 |
Details | BINDING: BINDING => ECO:0000255|HAMAP-Rule:MF_03215, ECO:0000269|Ref.7 |
Chain | Residue | Details |
A | ASN199 | |
B | ASN295 | |
A | THR235 | |
A | THR256 | |
A | GLY268 | |
A | ASN295 | |
B | ASN199 | |
B | THR235 | |
B | THR256 | |
B | GLY268 |
site_id | SWS_FT_FI4 |
Number of Residues | 8 |
Details | BINDING: BINDING => ECO:0000255|HAMAP-Rule:MF_03215, ECO:0000305|Ref.7 |
Chain | Residue | Details |
A | ASP263 | |
A | SER301 | |
A | ALA304 | |
A | SER310 | |
B | ASP263 | |
B | SER301 | |
B | ALA304 | |
B | SER310 |