Research workbench
Three-dimensional structure of a post translational modified barley LTP1
Analyse Three-dimensional structure of a post translational modified barley LTP1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3GSH
- Type
- protein
- Length
- 182 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Non-specific lipid-transfer protein 1
- UniProt
- P07597
- Ligands
- ASY, ZN, NA
- Pockets
- 2 · best druggability 0.64
Structure
x-ray diffraction · 1 distinct chain · 62% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Non-specific lipid-transfer protein 1 | protein | 91 | 62% helix, 0% strand | P07597 |
Ligands and binding sites
- ASY · (12E)-10-oxooctadec-12-enoic acid · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 4 copies · chains A, B
- NA · Sodium ion · metal · 3 copies · chains A, B
- TFA · trifluoroacetic acid · additive · 2 copies · chains A, B
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 | 69 | 0.64 | 0.92 | 14 | ASY |
| 2 | 244 | 0.64 | 0.82 | 40 | ZN, TFA, NA, ASY |
Interfaces
1 interface between chains.
- A–B · 396 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 2 covalent (disulfide, covalent ligand).
Compared structures
- 3GSH · Three-dimensional structure of a post translational modified barley LTP1 · the same entry in another collection · chain A against A, TM-score 1.00
- P07597 · AlphaFold monomer V2.0 prediction for non-specific lipid-transfer protein 1 (P07597) · a predicted model of the same protein · chain A against A, TM-score 0.95
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 P07597
- Elsewhere: RCSB PDB 3GSH · PDBe 3GSH · UniProt P07597
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