3B05
Crystal structure of Sulfolobus shibatae isopentenyl diphosphate isomerase in complex with reduced FMN and IPP at 2.2A resolution.
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0000287 | molecular_function | magnesium ion binding |
| A | 0004452 | molecular_function | isopentenyl-diphosphate delta-isomerase activity |
| A | 0005737 | cellular_component | cytoplasm |
| A | 0008299 | biological_process | isoprenoid biosynthetic process |
| A | 0010181 | molecular_function | FMN binding |
| A | 0016491 | molecular_function | oxidoreductase activity |
| A | 0016853 | molecular_function | isomerase activity |
| A | 0046872 | molecular_function | metal ion binding |
| A | 0070402 | molecular_function | NADPH binding |
| B | 0000287 | molecular_function | magnesium ion binding |
| B | 0004452 | molecular_function | isopentenyl-diphosphate delta-isomerase activity |
| B | 0005737 | cellular_component | cytoplasm |
| B | 0008299 | biological_process | isoprenoid biosynthetic process |
| B | 0010181 | molecular_function | FMN binding |
| B | 0016491 | molecular_function | oxidoreductase activity |
| B | 0016853 | molecular_function | isomerase activity |
| B | 0046872 | molecular_function | metal ion binding |
| B | 0070402 | molecular_function | NADPH binding |
| C | 0000287 | molecular_function | magnesium ion binding |
| C | 0004452 | molecular_function | isopentenyl-diphosphate delta-isomerase activity |
| C | 0005737 | cellular_component | cytoplasm |
| C | 0008299 | biological_process | isoprenoid biosynthetic process |
| C | 0010181 | molecular_function | FMN binding |
| C | 0016491 | molecular_function | oxidoreductase activity |
| C | 0016853 | molecular_function | isomerase activity |
| C | 0046872 | molecular_function | metal ion binding |
| C | 0070402 | molecular_function | NADPH binding |
| D | 0000287 | molecular_function | magnesium ion binding |
| D | 0004452 | molecular_function | isopentenyl-diphosphate delta-isomerase activity |
| D | 0005737 | cellular_component | cytoplasm |
| D | 0008299 | biological_process | isoprenoid biosynthetic process |
| D | 0010181 | molecular_function | FMN binding |
| D | 0016491 | molecular_function | oxidoreductase activity |
| D | 0016853 | molecular_function | isomerase activity |
| D | 0046872 | molecular_function | metal ion binding |
| D | 0070402 | molecular_function | NADPH binding |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 23 |
| Details | BINDING SITE FOR RESIDUE FNR A 669 |
| Chain | Residue |
| A | THR65 |
| A | GLY222 |
| A | THR223 |
| A | TRP225 |
| A | GLY274 |
| A | GLY275 |
| A | ARG277 |
| A | MET295 |
| A | ALA296 |
| A | LEU297 |
| A | HOH374 |
| A | GLY66 |
| A | HOH401 |
| A | HOH457 |
| A | HOH479 |
| A | IPE701 |
| A | MET67 |
| A | GLY95 |
| A | SER96 |
| A | ASN125 |
| A | HIS155 |
| A | LYS193 |
| A | SER218 |
| site_id | AC2 |
| Number of Residues | 16 |
| Details | BINDING SITE FOR RESIDUE IPE A 701 |
| Chain | Residue |
| A | ARG7 |
| A | LYS8 |
| A | HIS11 |
| A | SER96 |
| A | ARG98 |
| A | HIS155 |
| A | ASN157 |
| A | GLN160 |
| A | GLU161 |
| A | GLN164 |
| A | TRP225 |
| A | HOH371 |
| A | HOH437 |
| A | HOH467 |
| A | FNR669 |
| A | MG1001 |
| site_id | AC3 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE MG A 1001 |
| Chain | Residue |
| A | GLU161 |
| A | HOH371 |
| A | HOH437 |
| A | IPE701 |
| site_id | AC4 |
| Number of Residues | 22 |
| Details | BINDING SITE FOR RESIDUE FNR B 669 |
| Chain | Residue |
| B | THR65 |
| B | GLY66 |
| B | MET67 |
| B | GLY95 |
| B | SER96 |
| B | ASN125 |
| B | HIS155 |
| B | LYS193 |
| B | SER218 |
| B | GLY222 |
| B | THR223 |
| B | TRP225 |
| B | GLY274 |
| B | GLY275 |
| B | ARG277 |
| B | ALA296 |
| B | LEU297 |
| B | HOH370 |
| B | HOH380 |
| B | HOH384 |
| B | HOH469 |
| B | IPE701 |
| site_id | AC5 |
| Number of Residues | 15 |
| Details | BINDING SITE FOR RESIDUE IPE B 701 |
| Chain | Residue |
| B | ILE4 |
| B | ARG7 |
| B | LYS8 |
| B | HIS11 |
| B | SER96 |
| B | ARG98 |
| B | HIS155 |
| B | ASN157 |
| B | GLN160 |
| B | GLU161 |
| B | GLN164 |
| B | TRP225 |
| B | HOH446 |
| B | FNR669 |
| B | MG1001 |
| site_id | AC6 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE MG B 1001 |
| Chain | Residue |
| B | GLU161 |
| B | IPE701 |
| site_id | AC7 |
| Number of Residues | 22 |
| Details | BINDING SITE FOR RESIDUE FNR C 669 |
| Chain | Residue |
| C | HOH369 |
| C | HOH370 |
| C | HOH399 |
| C | HOH446 |
| C | IPE701 |
| C | THR65 |
| C | GLY66 |
| C | MET67 |
| C | GLY95 |
| C | SER96 |
| C | ASN125 |
| C | HIS155 |
| C | LYS193 |
| C | SER218 |
| C | GLY222 |
| C | THR223 |
| C | TRP225 |
| C | GLY274 |
| C | GLY275 |
| C | ARG277 |
| C | ALA296 |
| C | LEU297 |
| site_id | AC8 |
| Number of Residues | 18 |
| Details | BINDING SITE FOR RESIDUE IPE C 701 |
| Chain | Residue |
| C | ARG7 |
| C | LYS8 |
| C | HIS11 |
| C | SER96 |
| C | ARG98 |
| C | HIS155 |
| C | ASN157 |
| C | GLN160 |
| C | GLU161 |
| C | GLN164 |
| C | SER195 |
| C | TRP225 |
| C | HOH455 |
| C | HOH458 |
| C | HOH474 |
| C | HOH482 |
| C | FNR669 |
| C | MG1001 |
| site_id | AC9 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE MG C 1001 |
| Chain | Residue |
| C | GLU161 |
| C | HOH458 |
| C | HOH482 |
| C | IPE701 |
| site_id | BC1 |
| Number of Residues | 22 |
| Details | BINDING SITE FOR RESIDUE FNR D 669 |
| Chain | Residue |
| D | THR65 |
| D | GLY66 |
| D | MET67 |
| D | GLY95 |
| D | SER96 |
| D | ASN125 |
| D | HIS155 |
| D | LYS193 |
| D | SER218 |
| D | GLY222 |
| D | THR223 |
| D | TRP225 |
| D | GLY275 |
| D | ARG277 |
| D | ALA296 |
| D | LEU297 |
| D | LEU300 |
| D | HOH370 |
| D | HOH371 |
| D | HOH379 |
| D | HOH450 |
| D | IPE701 |
| site_id | BC2 |
| Number of Residues | 19 |
| Details | BINDING SITE FOR RESIDUE IPE D 701 |
| Chain | Residue |
| D | ILE4 |
| D | ARG7 |
| D | LYS8 |
| D | HIS11 |
| D | SER96 |
| D | ARG98 |
| D | HIS155 |
| D | ASN157 |
| D | GLN160 |
| D | GLU161 |
| D | GLN164 |
| D | TRP225 |
| D | HOH429 |
| D | HOH474 |
| D | HOH475 |
| D | HOH476 |
| D | HOH481 |
| D | FNR669 |
| D | MG1001 |
| site_id | BC3 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE MG D 1001 |
| Chain | Residue |
| D | ARG98 |
| D | GLU161 |
| D | HOH475 |
| D | HOH476 |
| D | HOH481 |
| D | IPE701 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 16 |
| Details | Binding site: {} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI2 |
| Number of Residues | 48 |
| Details | Binding site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_00354","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"19158086","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"22158896","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
