7ER7
Crystal structure of hyman Biliverdin IX-beta reductase B with Tamibarotene (A80)
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0003824 | molecular_function | catalytic activity |
| A | 0004074 | molecular_function | biliverdin reductase [NAD(P)+] activity |
| A | 0005515 | molecular_function | protein binding |
| A | 0005654 | cellular_component | nucleoplasm |
| A | 0005737 | cellular_component | cytoplasm |
| A | 0005829 | cellular_component | cytosol |
| A | 0005886 | cellular_component | plasma membrane |
| A | 0016491 | molecular_function | oxidoreductase activity |
| A | 0016740 | molecular_function | transferase activity |
| A | 0030219 | biological_process | megakaryocyte differentiation |
| A | 0035605 | molecular_function | peptidyl-cysteine S-nitrosylase activity |
| A | 0042167 | biological_process | heme catabolic process |
| A | 0042602 | molecular_function | riboflavin reductase (NADPH) activity |
| A | 0043231 | cellular_component | intracellular membrane-bounded organelle |
| A | 0046627 | biological_process | negative regulation of insulin receptor signaling pathway |
| A | 0052873 | molecular_function | FMN reductase (NADPH) activity |
| A | 0052874 | molecular_function | FMN reductase (NADH) activity |
| A | 0070062 | cellular_component | extracellular exosome |
| B | 0003824 | molecular_function | catalytic activity |
| B | 0004074 | molecular_function | biliverdin reductase [NAD(P)+] activity |
| B | 0005515 | molecular_function | protein binding |
| B | 0005654 | cellular_component | nucleoplasm |
| B | 0005737 | cellular_component | cytoplasm |
| B | 0005829 | cellular_component | cytosol |
| B | 0005886 | cellular_component | plasma membrane |
| B | 0016491 | molecular_function | oxidoreductase activity |
| B | 0016740 | molecular_function | transferase activity |
| B | 0030219 | biological_process | megakaryocyte differentiation |
| B | 0035605 | molecular_function | peptidyl-cysteine S-nitrosylase activity |
| B | 0042167 | biological_process | heme catabolic process |
| B | 0042602 | molecular_function | riboflavin reductase (NADPH) activity |
| B | 0043231 | cellular_component | intracellular membrane-bounded organelle |
| B | 0046627 | biological_process | negative regulation of insulin receptor signaling pathway |
| B | 0052873 | molecular_function | FMN reductase (NADPH) activity |
| B | 0052874 | molecular_function | FMN reductase (NADH) activity |
| B | 0070062 | cellular_component | extracellular exosome |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 36 |
| Details | binding site for residue NAP A 401 |
| Chain | Residue |
| A | GLY10 |
| A | LEU74 |
| A | LEU75 |
| A | GLY76 |
| A | ARG78 |
| A | VAL86 |
| A | MET87 |
| A | CYS109 |
| A | THR110 |
| A | HIS132 |
| A | PRO151 |
| A | THR12 |
| A | PRO152 |
| A | HIS153 |
| A | ILE154 |
| A | A80402 |
| A | HOH508 |
| A | HOH515 |
| A | HOH528 |
| A | HOH548 |
| A | HOH556 |
| A | HOH560 |
| A | GLY13 |
| A | HOH565 |
| A | HOH576 |
| A | HOH594 |
| A | HOH595 |
| A | HOH600 |
| B | SER82 |
| B | HOH538 |
| A | GLN14 |
| A | THR15 |
| A | ARG35 |
| A | ARG39 |
| A | ASP54 |
| A | VAL55 |
| site_id | AC2 |
| Number of Residues | 11 |
| Details | binding site for residue A80 A 402 |
| Chain | Residue |
| A | MET1 |
| A | LEU81 |
| A | PHE113 |
| A | TRP116 |
| A | PRO152 |
| A | HIS153 |
| A | ARG170 |
| A | ARG174 |
| A | TYR200 |
| A | NAP401 |
| A | HOH548 |
| site_id | AC3 |
| Number of Residues | 5 |
| Details | binding site for residue SO4 A 403 |
| Chain | Residue |
| A | SER173 |
| A | ARG174 |
| A | HOH509 |
| A | HOH525 |
| A | HOH531 |
| site_id | AC4 |
| Number of Residues | 26 |
| Details | binding site for residue NAP B 401 |
| Chain | Residue |
| A | ASP36 |
| A | SER38 |
| A | HOH501 |
| B | GLY10 |
| B | THR12 |
| B | GLY13 |
| B | GLN14 |
| B | THR15 |
| B | ARG35 |
| B | ARG39 |
| B | ASP54 |
| B | VAL55 |
| B | LEU75 |
| B | GLY76 |
| B | ARG78 |
| B | CYS109 |
| B | THR110 |
| B | SER111 |
| B | HIS132 |
| B | PRO151 |
| B | PRO152 |
| B | ILE154 |
| B | SO4406 |
| B | HOH511 |
| B | HOH563 |
| B | HOH572 |
| site_id | AC5 |
| Number of Residues | 9 |
| Details | binding site for residue SO4 B 402 |
| Chain | Residue |
| A | ARG140 |
| A | HOH616 |
| B | HIS153 |
| B | GLY155 |
| B | ASP156 |
| B | GLN157 |
| B | VAL175 |
| B | HOH507 |
| B | HOH546 |
| site_id | AC6 |
| Number of Residues | 4 |
| Details | binding site for residue SO4 B 403 |
| Chain | Residue |
| A | ALA48 |
| A | HIS49 |
| B | LYS137 |
| B | HOH501 |
| site_id | AC7 |
| Number of Residues | 3 |
| Details | binding site for residue SO4 B 404 |
| Chain | Residue |
| A | HIS183 |
| B | LYS4 |
| B | HOH512 |
| site_id | AC8 |
| Number of Residues | 3 |
| Details | binding site for residue SO4 B 405 |
| Chain | Residue |
| B | ALA26 |
| B | TYR28 |
| B | HOH509 |
| site_id | AC9 |
| Number of Residues | 5 |
| Details | binding site for residue SO4 B 406 |
| Chain | Residue |
| B | HIS153 |
| B | NAP401 |
| B | HOH529 |
| A | ARG134 |
| B | ARG78 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 4 |
| Details | ACT_SITE: S-nitroso-cysteine intermediate; for S-nitroso-CoA-dependent nitrosyltransferase activity => ECO:0000269|PubMed:38056462 |
| Chain | Residue | Details |
| A | CYS109 | |
| A | CYS188 | |
| B | CYS109 | |
| B | CYS188 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 2 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:11224564, ECO:0000269|PubMed:29487133, ECO:0000269|PubMed:34957824, ECO:0007744|PDB:1HDO, ECO:0007744|PDB:5OOG, ECO:0007744|PDB:5OOH, ECO:0007744|PDB:7ER7 |
| Chain | Residue | Details |
| A | GLY10 | |
| B | GLY10 |
| site_id | SWS_FT_FI3 |
| Number of Residues | 16 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:11224564, ECO:0000269|PubMed:29487133, ECO:0000269|PubMed:32246827, ECO:0000269|PubMed:34957824, ECO:0007744|PDB:1HDO, ECO:0007744|PDB:1HE2, ECO:0007744|PDB:1HE3, ECO:0007744|PDB:1HE4, ECO:0007744|PDB:1HE5, ECO:0007744|PDB:5OOG, ECO:0007744|PDB:5OOH, ECO:0007744|PDB:6OPL, ECO:0007744|PDB:7ER6, ECO:0007744|PDB:7ER7, ECO:0007744|PDB:7ER8, ECO:0007744|PDB:7ER9, ECO:0007744|PDB:7ERA, ECO:0007744|PDB:7ERB, ECO:0007744|PDB:7ERC, ECO:0007744|PDB:7ERD, ECO:0007744|PDB:7ERE |
| Chain | Residue | Details |
| A | THR12 | |
| B | THR15 | |
| B | ARG35 | |
| B | ASP54 | |
| B | VAL55 | |
| B | GLY76 | |
| B | ARG78 | |
| B | MET87 | |
| A | THR15 | |
| A | ARG35 | |
| A | ASP54 | |
| A | VAL55 | |
| A | GLY76 | |
| A | ARG78 | |
| A | MET87 | |
| B | THR12 |
| site_id | SWS_FT_FI4 |
| Number of Residues | 2 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:11224564, ECO:0000269|PubMed:32246827, ECO:0000269|PubMed:34957824, ECO:0007744|PDB:1HDO, ECO:0007744|PDB:1HE2, ECO:0007744|PDB:1HE3, ECO:0007744|PDB:1HE4, ECO:0007744|PDB:1HE5, ECO:0007744|PDB:5OOG, ECO:0007744|PDB:5OOH, ECO:0007744|PDB:6OPL, ECO:0007744|PDB:7ER6, ECO:0007744|PDB:7ER7, ECO:0007744|PDB:7ER8, ECO:0007744|PDB:7ER9, ECO:0007744|PDB:7ERA, ECO:0007744|PDB:7ERB, ECO:0007744|PDB:7ERC, ECO:0007744|PDB:7ERD, ECO:0007744|PDB:7ERE |
| Chain | Residue | Details |
| A | GLY13 | |
| B | GLY13 |
| site_id | SWS_FT_FI5 |
| Number of Residues | 4 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:11224564, ECO:0000269|PubMed:29487133, ECO:0000269|PubMed:34957824, ECO:0007744|PDB:1HDO, ECO:0007744|PDB:1HE2, ECO:0007744|PDB:1HE3, ECO:0007744|PDB:1HE4, ECO:0007744|PDB:1HE5, ECO:0007744|PDB:5OOG, ECO:0007744|PDB:5OOH, ECO:0007744|PDB:7ER6, ECO:0007744|PDB:7ER7, ECO:0007744|PDB:7ER8, ECO:0007744|PDB:7ER9, ECO:0007744|PDB:7ERA, ECO:0007744|PDB:7ERB, ECO:0007744|PDB:7ERC, ECO:0007744|PDB:7ERD, ECO:0007744|PDB:7ERE |
| Chain | Residue | Details |
| A | GLN14 | |
| A | ILE154 | |
| B | GLN14 | |
| B | ILE154 |
| site_id | SWS_FT_FI6 |
| Number of Residues | 2 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:34957824, ECO:0007744|PDB:7ER6, ECO:0007744|PDB:7ER9, ECO:0007744|PDB:7ERA, ECO:0007744|PDB:7ERB, ECO:0007744|PDB:7ERD, ECO:0007744|PDB:7ERE |
| Chain | Residue | Details |
| A | SER38 | |
| B | SER38 |
| site_id | SWS_FT_FI7 |
| Number of Residues | 2 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:29487133, ECO:0000269|PubMed:32246827, ECO:0000269|PubMed:34957824, ECO:0007744|PDB:5OOH, ECO:0007744|PDB:6OPL, ECO:0007744|PDB:7ER6, ECO:0007744|PDB:7ER7, ECO:0007744|PDB:7ER8, ECO:0007744|PDB:7ER9, ECO:0007744|PDB:7ERA, ECO:0007744|PDB:7ERB, ECO:0007744|PDB:7ERC, ECO:0007744|PDB:7ERE |
| Chain | Residue | Details |
| A | ARG39 | |
| B | ARG39 |
| site_id | SWS_FT_FI8 |
| Number of Residues | 2 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:11224564, ECO:0000269|PubMed:32246827, ECO:0000269|PubMed:34957824, ECO:0007744|PDB:1HDO, ECO:0007744|PDB:1HE2, ECO:0007744|PDB:1HE3, ECO:0007744|PDB:1HE4, ECO:0007744|PDB:1HE5, ECO:0007744|PDB:6OPL, ECO:0007744|PDB:7ER6, ECO:0007744|PDB:7ER7, ECO:0007744|PDB:7ER8, ECO:0007744|PDB:7ER9, ECO:0007744|PDB:7ERA, ECO:0007744|PDB:7ERB, ECO:0007744|PDB:7ERC, ECO:0007744|PDB:7ERD, ECO:0007744|PDB:7ERE |
| Chain | Residue | Details |
| A | LEU75 | |
| B | LEU75 |
| site_id | SWS_FT_FI9 |
| Number of Residues | 2 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:11224564, ECO:0000269|PubMed:29487133, ECO:0000269|PubMed:32246827, ECO:0000269|PubMed:34957824, ECO:0007744|PDB:1HDO, ECO:0007744|PDB:1HE2, ECO:0007744|PDB:1HE3, ECO:0007744|PDB:1HE4, ECO:0007744|PDB:1HE5, ECO:0007744|PDB:5OOH, ECO:0007744|PDB:6OPL, ECO:0007744|PDB:7ER6, ECO:0007744|PDB:7ER7, ECO:0007744|PDB:7ER8, ECO:0007744|PDB:7ER9, ECO:0007744|PDB:7ERA, ECO:0007744|PDB:7ERB, ECO:0007744|PDB:7ERC, ECO:0007744|PDB:7ERD, ECO:0007744|PDB:7ERE |
| Chain | Residue | Details |
| A | CYS109 | |
| B | CYS109 |
| site_id | SWS_FT_FI10 |
| Number of Residues | 2 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:11224564, ECO:0000269|PubMed:29487133, ECO:0000269|PubMed:32246827, ECO:0000269|PubMed:34957824, ECO:0007744|PDB:1HE3, ECO:0007744|PDB:5OOG, ECO:0007744|PDB:5OOH, ECO:0007744|PDB:6OPL, ECO:0007744|PDB:7ER8, ECO:0007744|PDB:7ER9, ECO:0007744|PDB:7ERB, ECO:0007744|PDB:7ERC |
| Chain | Residue | Details |
| A | HIS132 | |
| B | HIS132 |
| site_id | SWS_FT_FI11 |
| Number of Residues | 2 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:32246827, ECO:0000269|PubMed:34957824, ECO:0007744|PDB:6OPL, ECO:0007744|PDB:7ERB, ECO:0007744|PDB:7ERD |
| Chain | Residue | Details |
| A | HIS153 | |
| B | HIS153 |
| site_id | SWS_FT_FI12 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphoserine => ECO:0007744|PubMed:24275569 |
| Chain | Residue | Details |
| A | SER42 | |
| B | SER42 |
| site_id | SWS_FT_FI13 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphoserine => ECO:0007744|PubMed:23186163 |
| Chain | Residue | Details |
| A | SER82 | |
| B | SER82 |
