MolNFT v1 · #1764 · protein
Molecular structure of the bilin binding protein (bbp) from pieris brassicae after refinement at 2.0 ångströms resolution.
1BBP: “Molecular structure of the bilin binding protein (bbp) from pieris brassicae after refinement at 2.0…”. X-ray diffraction, 1 ligand (BLV), 9 pockets (best druggability 0.81). MolNFT v1 #1764 on GenesisL1: 3D structure, binding sites…
- 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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