Research workbench
Crystal structure of bnsp-7 from bothrops pauloensis complexed with cinnamic acid
Analyse Crystal structure of bnsp-7 from bothrops pauloensis complexed with cinnamic… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5VFN
- Type
- protein
- Length
- 242 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Basic phospholipase A2 homolog bnsp-7
- UniProt
- Q9IAT9
- Ligands
- ME2, HCI, SO4
- Pockets
- 1 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 48% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Basic phospholipase A2 homolog bnsp-7 | protein | 121 | 48% helix, 8% strand | Q9IAT9 |
Ligands and binding sites
- ME2 · 1-ethoxy-2-(2-methoxyethoxy)ethane · ligand · 2 copies · chains A, B
- HCI · Hydrocinnamic acid · ligand · chains A, B
- SO4 · Sulfate ion · ion · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 558 | 0.78 | 0.84 | 68 | ME2 |
Interfaces
1 interface between chains.
- A–B · 726 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide, 1 covalent (disulfide, covalent ligand).
Compared structures
- 5VFN · Crystal structure of BnSP-7 from Bothrops pauloensis complexed with cinnamic acid · the same entry in another collection · chain A against A, TM-score 1.00
- Q9IAT9 · AlphaFold monomer V2.0 prediction for basic phospholipase A2 homolog bnsp-7 (Q9IAT9) · a predicted model of the same protein · chain A 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 Q9IAT9
- Elsewhere: RCSB PDB 5VFN · PDBe 5VFN · UniProt Q9IAT9
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