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Structural insights into substrate binding of brown spider venom class II phospholipases D
Analyse Structural insights into substrate binding of brown spider venom class II… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4RW5
- Type
- protein
- Length
- 278 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phospholipase D lisictox-ALPHAIA1BII
- EC
- 3.1.4.4
- UniProt
- P0CE82
- Ligands
- PLM, TDA, OCA, MG
- Pockets
- 2 · best druggability 0.56
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phospholipase D lisictox-ALPHAIA1BII (EC 3.1.4.4) | protein | 278 | 38% helix, 20% strand | P0CE82 |
Ligands and binding sites
- PLM · Palmitic acid · ligand · chains A
- TDA · N-tridecanoic acid · ligand · chains A
- OCA · Octanoic acid (caprylic acid) · ligand · chains A
- MG · Magnesium ion · metal · chains A
- GOL · Glycerol · additive · chains 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 140 | 0.56 | 0.82 | 25 | MG, OCA |
| 2 | 60 | 0.33 | 0.77 | 13 | empty |
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 4RW5 · Structural insights into substrate binding of brown spider venom class II phospholipases D · the same entry in another collection · chain A against A, TM-score 1.00
- P0CE82 · AlphaFold monomer V2.0 prediction for dermonecrotic toxin lisictox- ALPHAIA1BII (P0CE82) · a predicted model of the same protein · 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
- Every structure of UniProt P0CE82
- Elsewhere: RCSB PDB 4RW5 · PDBe 4RW5 · UniProt P0CE82
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