Research workbench
Crystal structures of cadmium-binding acidic phospholipase A2 from the venom of agkistrodon halys pallas at 1.9 resolution (crystal grown at pH 5.9)
Analyse Crystal structures of cadmium-binding acidic phospholipase A2 from the venom of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1M8S
- Type
- protein
- Length
- 124 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phospholipase A2
- EC
- 3.1.1.4
- UniProt
- P14418
- Ligands
- CD
- Pockets
- 1 · best druggability 0.56
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phospholipase A2 (EC 3.1.1.4) | protein | 124 | 47% helix, 9% strand | P14418 |
Ligands and binding sites
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 | 172 | 0.56 | 0.80 | 21 | BU1 |
Modifications
Observed in the structure: 7 disulfide (disulfide).
Compared structures
- 1M8S · Crystal Structures of Cadmium-binding Acidic Phospholipase A2 from the Venom of… · the same entry in another collection · chain A against A, TM-score 1.00
- P14418 · AlphaFold monomer V2.0 prediction for acidic phospholipase A2 (P14418) · 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 P14418
- Elsewhere: RCSB PDB 1M8S · PDBe 1M8S · UniProt P14418
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