Research workbench
Structure of an acidic phospholipase A2 from the venom of ophiophagus hannah at 2.1 resolution from a hemihedrally twinned crystal form
Analyse Structure of an acidic phospholipase A2 from the venom of ophiophagus hannah at… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1M8T
- Type
- protein
- Length
- 714 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phospholipase A2
- EC
- 3.1.1.4
- UniProt
- Q9DF33
- Ligands
- CA
- Pockets
- 6 · best druggability 0.53
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Phospholipase A2 (EC 3.1.1.4) | protein | 119 | 47% helix, 9% strand | Q9DF33 |
Ligands and binding sites
- CA · Calcium ion · metal · 6 copies · chains A, B, C, D, E, F
- HEZ · Hexane-1,6-diol · additive · 10 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 155 | 0.53 | 0.80 | 19 | empty |
| 2 | 142 | 0.53 | 0.80 | 19 | empty |
| 3 | 137 | 0.53 | 0.80 | 19 | HEZ |
| 4 | 148 | 0.51 | 0.79 | 20 | empty |
| 5 | 129 | 0.51 | 0.80 | 19 | empty |
Modifications
Observed in the structure: 42 disulfide (disulfide).
Compared structures
- 1M8T · Structure of an acidic Phospholipase A2 from the venom of Ophiophagus hannah at 2.1… · the same entry in another collection · chain C against C, TM-score 1.00
- Q9DF33 · AlphaFold monomer V2.0 prediction for acidic phospholipase A2 2 (Q9DF33) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q9DF33
- Elsewhere: RCSB PDB 1M8T · PDBe 1M8T · UniProt Q9DF33
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.