MolNFT v1 · #39658 · protein
Crystal structures of phospholipases A2 from vipera nikolskii venom revealing triton X-100 bound in hydrophobic channel
2I0U · Basic subunit of heterodimer phospholipase A2: “Crystal structures of phospholipases A2 from vipera nikolskii venom revealing triton X-100 bound in…”. X-ray diffraction, 3 ligands (TRT, CA, SO4), 2 pockets (best druggability 0.59).…
- PDB
- 2I0U
- Type
- protein
- Length
- 244 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Basic subunit of heterodimer phospholipase A2
- EC
- 3.1.1.4
- UniProt
- Q1RP79
- Ligands
- TRT, CA, SO4
- Pockets
- 2 · best druggability 0.59
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E, A | Basic subunit of heterodimer phospholipase A2 (EC 3.1.1.4) | protein | 122 | 46% helix, 9% strand | Q1RP79 |
Ligands and binding sites
- TRT · Fragment of triton X-100 · ligand · 2 copies · chains E, A
- CA · Calcium ion · metal · 2 copies · chains E, A
- SO4 · Sulfate ion · ion · 2 copies · chains E, A
- TFA · trifluoroacetic acid · additive · chains E, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 245 | 0.59 | 0.79 | 23 | TRT |
| 2 | 166 | 0.54 | 0.79 | 21 | TRT |
Interfaces
1 interface between chains.
- E–A · 285 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide (disulfide).
Compared structures
- 2I0U · Crystal structures of phospholipases A2 from Vipera nikolskii venom revealing Triton… · the same entry in another collection · chain E against E, TM-score 1.00
- Q1RP79 · AlphaFold monomer V2.0 prediction for basic phospholipase A2 chain hdp-1P (Q1RP79) · a predicted model of the same protein · chain E 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 Q1RP79
- Elsewhere: RCSB PDB 2I0U · PDBe 2I0U · UniProt Q1RP79
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