Research workbench
Crystal structure of biliverdin reductase in complex with NADP+ from synechocystis sp. pcc 6803
Analyse Crystal structure of biliverdin reductase in complex with NADP+ from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5B3U
- Type
- protein
- Length
- 634 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Biliverdin reductase
- UniProt
- P72782
- Ligands
- NAP, PO4
- Pockets
- 5 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Biliverdin reductase | protein | 317 | 36% helix, 32% strand | P72782 |
| B | Biliverdin reductase | protein | 317 | 39% helix, 30% strand | P72782 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · chains B
- PO4 · Phosphate ion · ion · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 865 | 0.77 | 0.81 | 110 | PO4 |
| 2 | 575 | 0.69 | 0.78 | 53 | NAP, PO4 |
| 3 | 135 | 0.44 | 0.76 | 28 | empty |
| 4 | 76 | 0.34 | 0.75 | 13 | empty |
| 5 | 76 | 0.32 | 0.74 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 323 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5B3U · Crystal structure of biliverdin reductase in complex with NADP+ from Synechocystis sp.… · the same entry in another collection · chain A against A, TM-score 1.00
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 P72782
- Elsewhere: RCSB PDB 5B3U · PDBe 5B3U · UniProt P72782
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