3A9C
Crystal structure of ribose-1,5-bisphosphate isomerase from Thermococcus kodakaraensis KOD1 in complex with ribulose-1,5-bisphosphate
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0016853 | molecular_function | isomerase activity |
| A | 0019323 | biological_process | pentose catabolic process |
| A | 0019509 | biological_process | L-methionine salvage from methylthioadenosine |
| A | 0043917 | molecular_function | ribose 1,5-bisphosphate isomerase activity |
| A | 0044237 | biological_process | cellular metabolic process |
| A | 0044249 | biological_process | cellular biosynthetic process |
| A | 0046523 | molecular_function | S-methyl-5-thioribose-1-phosphate isomerase activity |
| B | 0016853 | molecular_function | isomerase activity |
| B | 0019323 | biological_process | pentose catabolic process |
| B | 0019509 | biological_process | L-methionine salvage from methylthioadenosine |
| B | 0043917 | molecular_function | ribose 1,5-bisphosphate isomerase activity |
| B | 0044237 | biological_process | cellular metabolic process |
| B | 0044249 | biological_process | cellular biosynthetic process |
| B | 0046523 | molecular_function | S-methyl-5-thioribose-1-phosphate isomerase activity |
| C | 0016853 | molecular_function | isomerase activity |
| C | 0019323 | biological_process | pentose catabolic process |
| C | 0019509 | biological_process | L-methionine salvage from methylthioadenosine |
| C | 0043917 | molecular_function | ribose 1,5-bisphosphate isomerase activity |
| C | 0044237 | biological_process | cellular metabolic process |
| C | 0044249 | biological_process | cellular biosynthetic process |
| C | 0046523 | molecular_function | S-methyl-5-thioribose-1-phosphate isomerase activity |
| D | 0016853 | molecular_function | isomerase activity |
| D | 0019323 | biological_process | pentose catabolic process |
| D | 0019509 | biological_process | L-methionine salvage from methylthioadenosine |
| D | 0043917 | molecular_function | ribose 1,5-bisphosphate isomerase activity |
| D | 0044237 | biological_process | cellular metabolic process |
| D | 0044249 | biological_process | cellular biosynthetic process |
| D | 0046523 | molecular_function | S-methyl-5-thioribose-1-phosphate isomerase activity |
| E | 0016853 | molecular_function | isomerase activity |
| E | 0019323 | biological_process | pentose catabolic process |
| E | 0019509 | biological_process | L-methionine salvage from methylthioadenosine |
| E | 0043917 | molecular_function | ribose 1,5-bisphosphate isomerase activity |
| E | 0044237 | biological_process | cellular metabolic process |
| E | 0044249 | biological_process | cellular biosynthetic process |
| E | 0046523 | molecular_function | S-methyl-5-thioribose-1-phosphate isomerase activity |
| F | 0016853 | molecular_function | isomerase activity |
| F | 0019323 | biological_process | pentose catabolic process |
| F | 0019509 | biological_process | L-methionine salvage from methylthioadenosine |
| F | 0043917 | molecular_function | ribose 1,5-bisphosphate isomerase activity |
| F | 0044237 | biological_process | cellular metabolic process |
| F | 0044249 | biological_process | cellular biosynthetic process |
| F | 0046523 | molecular_function | S-methyl-5-thioribose-1-phosphate isomerase activity |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 11 |
| Details | BINDING SITE FOR RESIDUE RUB A 401 |
| Chain | Residue |
| A | CSD133 |
| A | HOH601 |
| A | HOH614 |
| A | SER135 |
| A | LYS136 |
| A | ALA137 |
| A | ALA201 |
| A | ASN212 |
| A | LYS213 |
| A | LYS238 |
| A | ARG254 |
| site_id | AC2 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE PEG A 402 |
| Chain | Residue |
| A | LYS224 |
| A | VAL228 |
| A | GLU285 |
| A | ASP288 |
| site_id | AC3 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE MG A 411 |
| Chain | Residue |
| A | ASP304 |
| E | ASP304 |
| site_id | AC4 |
| Number of Residues | 13 |
| Details | BINDING SITE FOR RESIDUE RUB B 401 |
| Chain | Residue |
| B | CSD133 |
| B | SER135 |
| B | LYS136 |
| B | ALA137 |
| B | ALA201 |
| B | ASP202 |
| B | ASN212 |
| B | LYS213 |
| B | LYS238 |
| B | ARG254 |
| B | HOH601 |
| B | HOH603 |
| B | HOH615 |
| site_id | AC5 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE PEG B 402 |
| Chain | Residue |
| B | ALA223 |
| B | LYS224 |
| B | ARG227 |
| B | VAL228 |
| B | THR230 |
| B | TYR286 |
| B | ASP288 |
| site_id | AC6 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE MG B 411 |
| Chain | Residue |
| B | ASP304 |
| D | ASP304 |
| site_id | AC7 |
| Number of Residues | 12 |
| Details | BINDING SITE FOR RESIDUE RUB C 401 |
| Chain | Residue |
| C | CSD133 |
| C | SER135 |
| C | LYS136 |
| C | ALA137 |
| C | GLN164 |
| C | ALA201 |
| C | ASN212 |
| C | LYS213 |
| C | LYS238 |
| C | ARG254 |
| C | HOH601 |
| C | HOH609 |
| site_id | AC8 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE PEG C 402 |
| Chain | Residue |
| C | LYS224 |
| C | VAL228 |
| C | GLU285 |
| C | TYR286 |
| C | ASP288 |
| site_id | AC9 |
| Number of Residues | 13 |
| Details | BINDING SITE FOR RESIDUE RUB D 401 |
| Chain | Residue |
| D | CSD133 |
| D | SER135 |
| D | LYS136 |
| D | ALA137 |
| D | GLN164 |
| D | ALA201 |
| D | ASN212 |
| D | LYS213 |
| D | LYS238 |
| D | ARG254 |
| D | HOH601 |
| D | HOH620 |
| D | HOH627 |
| site_id | BC1 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE PEG D 402 |
| Chain | Residue |
| D | LYS224 |
| D | ARG227 |
| D | VAL228 |
| D | TYR286 |
| D | ASP288 |
| D | HOH619 |
| site_id | BC2 |
| Number of Residues | 12 |
| Details | BINDING SITE FOR RESIDUE RUB E 401 |
| Chain | Residue |
| E | CSD133 |
| E | SER135 |
| E | LYS136 |
| E | ALA137 |
| E | GLN164 |
| E | ALA201 |
| E | ASN212 |
| E | LYS213 |
| E | LYS238 |
| E | ARG254 |
| E | HOH601 |
| E | HOH618 |
| site_id | BC3 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE PEG E 402 |
| Chain | Residue |
| E | LYS224 |
| E | ARG227 |
| E | VAL228 |
| E | TRP229 |
| E | ASP288 |
| site_id | BC4 |
| Number of Residues | 11 |
| Details | BINDING SITE FOR RESIDUE RUB F 401 |
| Chain | Residue |
| F | LYS238 |
| F | ARG254 |
| F | HOH601 |
| F | HOH633 |
| F | CSD133 |
| F | SER135 |
| F | LYS136 |
| F | ALA137 |
| F | LYS162 |
| F | ASN212 |
| F | LYS213 |
| site_id | BC5 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE PEG F 402 |
| Chain | Residue |
| F | LYS224 |
| F | ARG227 |
| F | VAL228 |
| F | THR230 |
| F | ASP288 |
| F | HOH637 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 6 |
| Details | ACT_SITE: Proton acceptor => ECO:0000255|HAMAP-Rule:MF_02230, ECO:0000269|PubMed:22511789 |
| Chain | Residue | Details |
| A | CSD133 | |
| B | CSD133 | |
| C | CSD133 | |
| D | CSD133 | |
| E | CSD133 | |
| F | CSD133 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 6 |
| Details | ACT_SITE: Proton donor => ECO:0000255|HAMAP-Rule:MF_02230, ECO:0000269|PubMed:22511789 |
| Chain | Residue | Details |
| A | ASP202 | |
| B | ASP202 | |
| C | ASP202 | |
| D | ASP202 | |
| E | ASP202 | |
| F | ASP202 |
| site_id | SWS_FT_FI3 |
| Number of Residues | 18 |
| Details | BINDING: BINDING => ECO:0000255|HAMAP-Rule:MF_02230 |
| Chain | Residue | Details |
| A | ARG20 | |
| D | ARG20 | |
| D | SER135 | |
| D | ASN212 | |
| E | ARG20 | |
| E | SER135 | |
| E | ASN212 | |
| F | ARG20 | |
| F | SER135 | |
| F | ASN212 | |
| A | SER135 | |
| A | ASN212 | |
| B | ARG20 | |
| B | SER135 | |
| B | ASN212 | |
| C | ARG20 | |
| C | SER135 | |
| C | ASN212 |
| site_id | SWS_FT_FI4 |
| Number of Residues | 12 |
| Details | BINDING: BINDING => ECO:0000255|HAMAP-Rule:MF_02230, ECO:0000269|PubMed:22511789 |
| Chain | Residue | Details |
| A | ARG63 | |
| E | LYS238 | |
| F | ARG63 | |
| F | LYS238 | |
| A | LYS238 | |
| B | ARG63 | |
| B | LYS238 | |
| C | ARG63 | |
| C | LYS238 | |
| D | ARG63 | |
| D | LYS238 | |
| E | ARG63 |
| site_id | SWS_FT_FI5 |
| Number of Residues | 6 |
| Details | SITE: Plays a key role in hexamerization |
| Chain | Residue | Details |
| A | ARG227 | |
| B | ARG227 | |
| C | ARG227 | |
| D | ARG227 | |
| E | ARG227 | |
| F | ARG227 |
