3JR2
X-ray crystal structure of the Mg-bound 3-keto-L-gulonate-6-phosphate decarboxylase from Vibrio cholerae O1 biovar El Tor str. N16961
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0004590 | molecular_function | orotidine-5'-phosphate decarboxylase activity |
| A | 0005975 | biological_process | carbohydrate metabolic process |
| A | 0006207 | biological_process | 'de novo' pyrimidine nucleobase biosynthetic process |
| A | 0016829 | molecular_function | lyase activity |
| A | 0019854 | biological_process | L-ascorbic acid catabolic process |
| A | 0033982 | molecular_function | 3-dehydro-L-gulonate-6-phosphate decarboxylase activity |
| A | 0046872 | molecular_function | metal ion binding |
| B | 0004590 | molecular_function | orotidine-5'-phosphate decarboxylase activity |
| B | 0005975 | biological_process | carbohydrate metabolic process |
| B | 0006207 | biological_process | 'de novo' pyrimidine nucleobase biosynthetic process |
| B | 0016829 | molecular_function | lyase activity |
| B | 0019854 | biological_process | L-ascorbic acid catabolic process |
| B | 0033982 | molecular_function | 3-dehydro-L-gulonate-6-phosphate decarboxylase activity |
| B | 0046872 | molecular_function | metal ion binding |
| C | 0004590 | molecular_function | orotidine-5'-phosphate decarboxylase activity |
| C | 0005975 | biological_process | carbohydrate metabolic process |
| C | 0006207 | biological_process | 'de novo' pyrimidine nucleobase biosynthetic process |
| C | 0016829 | molecular_function | lyase activity |
| C | 0019854 | biological_process | L-ascorbic acid catabolic process |
| C | 0033982 | molecular_function | 3-dehydro-L-gulonate-6-phosphate decarboxylase activity |
| C | 0046872 | molecular_function | metal ion binding |
| D | 0004590 | molecular_function | orotidine-5'-phosphate decarboxylase activity |
| D | 0005975 | biological_process | carbohydrate metabolic process |
| D | 0006207 | biological_process | 'de novo' pyrimidine nucleobase biosynthetic process |
| D | 0016829 | molecular_function | lyase activity |
| D | 0019854 | biological_process | L-ascorbic acid catabolic process |
| D | 0033982 | molecular_function | 3-dehydro-L-gulonate-6-phosphate decarboxylase activity |
| D | 0046872 | molecular_function | metal ion binding |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE EDO A 901 |
| Chain | Residue |
| A | ILE113 |
| A | TYR135 |
| A | HIS136 |
| A | HOH231 |
| site_id | AC2 |
| Number of Residues | 8 |
| Details | BINDING SITE FOR RESIDUE GOL A 1001 |
| Chain | Residue |
| A | HOH246 |
| A | HOH469 |
| A | HOH724 |
| A | ALA88 |
| A | ALA90 |
| A | ILE95 |
| A | ASP121 |
| A | TRP125 |
| site_id | AC3 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE GOL A 1002 |
| Chain | Residue |
| A | THR118 |
| A | MSE119 |
| A | GLN120 |
| site_id | AC4 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE GOL A 1003 |
| Chain | Residue |
| A | ARG51 |
| A | PRO55 |
| A | HIS57 |
| A | ASP82 |
| A | HOH498 |
| A | HOH687 |
| site_id | AC5 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE EDO A 902 |
| Chain | Residue |
| A | ASN56 |
| A | HOH245 |
| A | HOH743 |
| site_id | AC6 |
| Number of Residues | 9 |
| Details | BINDING SITE FOR RESIDUE SO4 A 501 |
| Chain | Residue |
| A | ASP67 |
| A | GLY68 |
| A | GLY69 |
| A | ALA70 |
| A | THR94 |
| A | ALA97 |
| A | HOH227 |
| A | HOH271 |
| B | ARG139 |
| site_id | AC7 |
| Number of Residues | 10 |
| Details | BINDING SITE FOR RESIDUE SO4 A 502 |
| Chain | Residue |
| A | GLY170 |
| A | GLY171 |
| A | ALA190 |
| A | GLY191 |
| A | HOH242 |
| A | HOH331 |
| A | HOH382 |
| A | HOH459 |
| A | HOH483 |
| A | HOH681 |
| site_id | AC8 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE MG A 3001 |
| Chain | Residue |
| A | GLU33 |
| A | ASP62 |
| A | GLU112 |
| A | HOH249 |
| A | HOH258 |
| A | HOH284 |
| A | HOH285 |
| site_id | AC9 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE MG A 3002 |
| Chain | Residue |
| A | HOH275 |
| A | HOH790 |
| A | HOH791 |
| A | HOH792 |
| A | HOH793 |
| A | HOH794 |
| site_id | BC1 |
| Number of Residues | 12 |
| Details | BINDING SITE FOR RESIDUE SO4 B 501 |
| Chain | Residue |
| A | ARG139 |
| B | ASP67 |
| B | GLY68 |
| B | GLY69 |
| B | ALA70 |
| B | THR94 |
| B | ALA97 |
| B | HOH242 |
| B | HOH467 |
| B | HOH479 |
| B | HOH503 |
| B | HOH553 |
| site_id | BC2 |
| Number of Residues | 9 |
| Details | BINDING SITE FOR RESIDUE SO4 B 502 |
| Chain | Residue |
| B | GLY171 |
| B | ALA190 |
| B | GLY191 |
| B | HOH220 |
| B | HOH258 |
| B | HOH269 |
| B | HOH337 |
| B | HOH355 |
| B | HOH435 |
| site_id | BC3 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE MG B 3001 |
| Chain | Residue |
| B | GLU33 |
| B | ASP62 |
| B | GLU112 |
| B | HOH239 |
| B | HOH249 |
| B | HOH302 |
| B | HOH304 |
| site_id | BC4 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE MG B 3002 |
| Chain | Residue |
| B | HIS52 |
| B | HOH531 |
| B | HOH774 |
| B | HOH775 |
| C | HOH266 |
| C | HOH505 |
| site_id | BC5 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE EDO C 901 |
| Chain | Residue |
| C | ALA88 |
| C | ALA90 |
| C | ILE92 |
| C | ILE95 |
| C | ASP121 |
| C | TRP125 |
| C | HOH264 |
| site_id | BC6 |
| Number of Residues | 1 |
| Details | BINDING SITE FOR RESIDUE EDO C 902 |
| Chain | Residue |
| C | ARG212 |
| site_id | BC7 |
| Number of Residues | 12 |
| Details | BINDING SITE FOR RESIDUE SO4 C 501 |
| Chain | Residue |
| C | GLY68 |
| C | GLY69 |
| C | ALA70 |
| C | ALA93 |
| C | THR94 |
| C | ALA97 |
| C | HOH229 |
| C | HOH438 |
| C | HOH639 |
| C | HOH642 |
| D | ARG139 |
| C | ASP67 |
| site_id | BC8 |
| Number of Residues | 9 |
| Details | BINDING SITE FOR RESIDUE SO4 C 502 |
| Chain | Residue |
| C | GLY170 |
| C | GLY171 |
| C | ALA190 |
| C | GLY191 |
| C | HOH217 |
| C | HOH396 |
| C | HOH474 |
| C | HOH500 |
| C | HOH694 |
| site_id | BC9 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE SO4 C 503 |
| Chain | Residue |
| C | THR13 |
| C | ASN14 |
| site_id | CC1 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE MG C 3002 |
| Chain | Residue |
| C | HIS136 |
| C | HOH269 |
| C | HOH272 |
| C | HOH273 |
| C | HOH274 |
| C | HOH276 |
| site_id | CC2 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE MG C 3001 |
| Chain | Residue |
| C | GLU33 |
| C | ASP62 |
| C | GLU112 |
| C | HOH230 |
| C | HOH255 |
| C | HOH258 |
| C | HOH271 |
| site_id | CC3 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE GOL D 1001 |
| Chain | Residue |
| D | ILE113 |
| D | TYR135 |
| D | HIS136 |
| D | SER138 |
| D | HOH221 |
| D | HOH231 |
| site_id | CC4 |
| Number of Residues | 8 |
| Details | BINDING SITE FOR RESIDUE GOL D 1002 |
| Chain | Residue |
| C | ARG139 |
| C | HOH269 |
| D | ASP67 |
| D | GLY68 |
| D | GLY69 |
| D | ALA70 |
| D | THR94 |
| D | HOH708 |
| site_id | CC5 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE EDO D 901 |
| Chain | Residue |
| D | ALA88 |
| D | ALA90 |
| D | TRP125 |
| site_id | CC6 |
| Number of Residues | 8 |
| Details | BINDING SITE FOR RESIDUE SO4 D 501 |
| Chain | Residue |
| D | GLY170 |
| D | GLY171 |
| D | ALA190 |
| D | GLY191 |
| D | HOH236 |
| D | HOH380 |
| D | HOH395 |
| D | HOH582 |
| site_id | CC7 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE MG D 3001 |
| Chain | Residue |
| D | GLU33 |
| D | ASP62 |
| D | HOH248 |
| D | HOH249 |
| D | HOH250 |
| D | HOH251 |
