Research workbench
Crystal structure of an acidic phospholipase A2 (btha-I) from bothrops jararacussu venom complexed with P-bromophenacyl bromide
Analyse Crystal structure of an acidic phospholipase A2 (btha-I) from bothrops… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1Z76
- Type
- protein
- Length
- 244 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phospholipase A2
- EC
- 3.1.1.4
- Ligands
- PBP
- Pockets
- 4 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 48% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Phospholipase A2 (EC 3.1.1.4) | protein | 122 | 48% helix, 9% strand | — |
Ligands and binding sites
- PBP · p-Bromophenacyl bromide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 130 | 0.74 | 0.93 | 22 | PBP |
| 2 | 465 | 0.69 | 0.80 | 35 | empty |
| 3 | 178 | 0.63 | 0.83 | 20 | PBP |
| 4 | 78 | 0.40 | 0.78 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 803 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide, 2 covalent (disulfide, covalent ligand).
Compared structures
- 1Z76 · Crystal structure of an acidic phospholipase A2 (BthA-I) from Bothrops jararacussu venom… · 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
- Elsewhere: RCSB PDB 1Z76 · PDBe 1Z76
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.