1JCL
OBSERVATION OF COVALENT INTERMEDIATES IN AN ENZYME MECHANISM AT ATOMIC RESOLUTION
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0003824 | molecular_function | catalytic activity |
| A | 0004139 | molecular_function | deoxyribose-phosphate aldolase activity |
| A | 0005737 | cellular_component | cytoplasm |
| A | 0005829 | cellular_component | cytosol |
| A | 0006018 | biological_process | 2-deoxyribose 1-phosphate catabolic process |
| A | 0006974 | biological_process | DNA damage response |
| A | 0009264 | biological_process | deoxyribonucleotide catabolic process |
| A | 0015949 | biological_process | nucleobase-containing small molecule interconversion |
| A | 0016020 | cellular_component | membrane |
| A | 0016052 | biological_process | carbohydrate catabolic process |
| A | 0016829 | molecular_function | lyase activity |
| A | 0046386 | biological_process | deoxyribose phosphate catabolic process |
| B | 0003824 | molecular_function | catalytic activity |
| B | 0004139 | molecular_function | deoxyribose-phosphate aldolase activity |
| B | 0005737 | cellular_component | cytoplasm |
| B | 0005829 | cellular_component | cytosol |
| B | 0006018 | biological_process | 2-deoxyribose 1-phosphate catabolic process |
| B | 0006974 | biological_process | DNA damage response |
| B | 0009264 | biological_process | deoxyribonucleotide catabolic process |
| B | 0015949 | biological_process | nucleobase-containing small molecule interconversion |
| B | 0016020 | cellular_component | membrane |
| B | 0016052 | biological_process | carbohydrate catabolic process |
| B | 0016829 | molecular_function | lyase activity |
| B | 0046386 | biological_process | deoxyribose phosphate catabolic process |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 16 |
| Details | BINDING SITE FOR RESIDUE HPD A 801 |
| Chain | Residue |
| A | CYS47 |
| A | SER238 |
| A | HOH814 |
| A | HOH817 |
| A | HOH829 |
| A | HOH901 |
| A | HOH927 |
| A | HOH1055 |
| A | VAL73 |
| A | LYS167 |
| A | THR170 |
| A | ALA203 |
| A | GLY204 |
| A | GLY205 |
| A | GLY236 |
| A | ALA237 |
| site_id | AC2 |
| Number of Residues | 17 |
| Details | BINDING SITE FOR RESIDUE HPD B 802 |
| Chain | Residue |
| B | LEU20 |
| B | CYS47 |
| B | VAL73 |
| B | LYS167 |
| B | THR170 |
| B | ALA203 |
| B | GLY204 |
| B | GLY205 |
| B | GLY236 |
| B | ALA237 |
| B | SER238 |
| B | HOH810 |
| B | HOH834 |
| B | HOH915 |
| B | HOH918 |
| B | HOH961 |
| B | HOH1027 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 2 |
| Details | ACT_SITE: Proton donor/acceptor => ECO:0000255|HAMAP-Rule:MF_00592, ECO:0000305|PubMed:11598300 |
| Chain | Residue | Details |
| A | ASP102 | |
| B | ASP102 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 2 |
| Details | ACT_SITE: Schiff-base intermediate with acetaldehyde => ECO:0000255|HAMAP-Rule:MF_00592, ECO:0000269|PubMed:11598300, ECO:0000305|PubMed:15476818 |
| Chain | Residue | Details |
| A | LYS167 | |
| B | LYS167 |
| site_id | SWS_FT_FI3 |
| Number of Residues | 2 |
| Details | ACT_SITE: Proton donor/acceptor => ECO:0000255|HAMAP-Rule:MF_00592, ECO:0000305|PubMed:11598300, ECO:0000305|PubMed:15476818 |
| Chain | Residue | Details |
| A | LYS201 | |
| B | LYS201 |
| site_id | SWS_FT_FI4 |
| Number of Residues | 2 |
| Details | MOD_RES: N6-acetyllysine => ECO:0000269|PubMed:18723842 |
| Chain | Residue | Details |
| A | LYS167 | |
| B | LYS167 |
Catalytic Information from CSA
| site_id | CSA1 |
| Number of Residues | 3 |
| Details | Annotated By Reference To The Literature 1p1x |
| Chain | Residue | Details |
| A | ASP102 | |
| A | LYS201 | |
| A | LYS167 |
| site_id | CSA2 |
| Number of Residues | 3 |
| Details | Annotated By Reference To The Literature 1p1x |
| Chain | Residue | Details |
| B | ASP102 | |
| B | LYS201 | |
| B | LYS167 |
| site_id | MCSA1 |
| Number of Residues | 3 |
| Details | M-CSA 613 |
| Chain | Residue | Details |
| A | ASP102 | increase nucleophilicity, proton acceptor, proton donor, proton relay |
| A | LYS167 | covalently attached, electron pair acceptor, electron pair donor, nucleofuge, nucleophile, proton acceptor, proton donor |
| A | LYS201 | increase nucleophilicity, proton acceptor, proton donor, proton relay |
| site_id | MCSA2 |
| Number of Residues | 3 |
| Details | M-CSA 613 |
| Chain | Residue | Details |
| B | ASP102 | increase nucleophilicity, proton acceptor, proton donor, proton relay |
| B | LYS167 | covalently attached, electron pair acceptor, electron pair donor, nucleofuge, nucleophile, proton acceptor, proton donor |
| B | LYS201 | increase nucleophilicity, proton acceptor, proton donor, proton relay |
