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Crystal structure of human biliverdin IX-beta reductase B with pyrantel pamoate (ppa)
Analyse Crystal structure of human biliverdin IX-beta reductase B with pyrantel pamoate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7ERE
- Type
- protein
- Length
- 826 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Flavin reductase (NADPH)
- EC
- 1.5.1.30, 1.3.1.24
- UniProt
- P30043
- Ligands
- NAP, JBR, SO4
- Pockets
- 6 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Flavin reductase (NADPH) (EC 1.5.1.30, 1.3.1.24) | protein | 207 | 36% helix, 21% strand | P30043 |
| B, D | Flavin reductase (NADPH) (EC 1.5.1.30, 1.3.1.24) | protein | 206 | 38% helix, 21% strand | P30043 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, D, B, C
- JBR · 4-[(3-carboxy-2-oxidanyl-naphthalen-1-yl)methyl]-3-oxidanyl-naphthalene-2-carboxylic acid · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 7 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1127 | 0.84 | 0.85 | 94 | NAP, JBR, SO4 |
| 2 | 1075 | 0.82 | 0.83 | 80 | JBR, NAP |
| 3 | 663 | 0.75 | 0.81 | 67 | NAP, JBR |
| 4 | 686 | 0.75 | 0.81 | 63 | NAP, JBR |
| 5 | 261 | 0.61 | 0.80 | 45 | empty |
Interfaces
6 interfaces between chains.
- B–C · 758 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 754 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 725 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 704 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 177 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 7ERE · Crystal structure of human Biliverdin IX-beta reductase B with Pyrantel Pamoate (PPA) · the same entry in another collection · chain D against D, TM-score 1.00
- P30043 · AlphaFold monomer V2.0 prediction for flavin reductase (NADPH) (P30043) · a predicted model of the same protein · chain B against A, TM-score 0.98
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P30043
- Elsewhere: RCSB PDB 7ERE · PDBe 7ERE · UniProt P30043
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