Research workbench
Molecular structure of the bilin binding protein (bbp) from pieris brassicae after refinement at 2.0 ångströms resolution.
Analyse Molecular structure of the bilin binding protein (bbp) from pieris brassicae… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1BBP
- Type
- protein
- Length
- 692 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bilin binding protein
- UniProt
- P09464
- Ligands
- BLV
- Pockets
- 9 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 13% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Bilin binding protein | protein | 173 | 13% helix, 48% strand | P09464 |
Ligands and binding sites
- BLV · Biliverdin IX gamma chromophore · ligand · 4 copies · chains A, C, B, 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 | 715 | 0.81 | 0.85 | 84 | BLV |
| 2 | 845 | 0.78 | 0.81 | 70 | empty |
| 3 | 722 | 0.75 | 0.80 | 60 | empty |
| 4 | 370 | 0.75 | 0.85 | 43 | BLV |
| 5 | 363 | 0.74 | 0.85 | 39 | BLV |
Interfaces
5 interfaces between chains.
- A–C · 954 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 905 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 522 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 512 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 283 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 1BBP · Molecular structure of the bilin binding protein (bbp) from pieris brassicae after… · the same entry in another collection · chain A against A, TM-score 1.00
- P09464 · AlphaFold monomer V2.0 prediction for bilin-binding protein (P09464) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 P09464
- Elsewhere: RCSB PDB 1BBP · PDBe 1BBP · UniProt P09464
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