MolNFT v1 · #114157 · protein
Crystal structure of biliverdin reductase in complex with biliverdin and NADP+ from synechocystis sp. pcc 6803
5B3V: “Crystal structure of biliverdin reductase in complex with biliverdin and NADP+ from synechocystis sp. pcc 6803”. X-ray diffraction, 2 ligands (BLA, NAP), 9 pockets (best druggability 0.79). MolNFT v1 #114157 on GenesisL1: 3D…
- PDB
- 5B3V
- Type
- protein
- Length
- 1,265 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Biliverdin reductase
- UniProt
- P72782
- Ligands
- BLA, NAP
- Pockets
- 9 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, C, D | Biliverdin reductase | protein | 316 | 40% helix, 31% strand | P72782 |
| A | Biliverdin reductase | protein | 317 | 38% helix, 31% strand | P72782 |
Ligands and binding sites
- BLA · Biliverdine IX alpha · ligand · 8 copies · chains B, A, C, D
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains B, A, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1150 | 0.79 | 0.81 | 108 | NAP, BLA |
| 2 | 643 | 0.70 | 0.78 | 56 | NAP, BLA |
| 3 | 661 | 0.69 | 0.77 | 57 | NAP, BLA |
| 4 | 674 | 0.68 | 0.76 | 63 | NAP, BLA |
| 5 | 425 | 0.59 | 0.75 | 41 | empty |
Interfaces
2 interfaces between chains.
- B–A · 760 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 131 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5B3V · Crystal structure of biliverdin reductase in complex with biliverdin and NADP+ from… · the same entry in another collection · chain B against B, 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 5B3V · PDBe 5B3V · UniProt P72782
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