Research workbench
Crystal structure of LS24, a seed albumin from lathyrus sativus
Analyse Crystal structure of LS24, a seed albumin from lathyrus sativus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3LP9
- Type
- protein
- Length
- 908 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ls-24
- Ligands
- SPM, CA, NA, CL
- Pockets
- 7 · best druggability 0.56
Structure
x-ray diffraction · 1 distinct chain · 16% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Ls-24 | protein | 227 | 16% helix, 40% strand | — |
Ligands and binding sites
- SPM · Spermine · ligand · chains B, D
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D
- NA · Sodium ion · metal · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 91 | 0.56 | 0.86 | 27 | empty |
| 2 | 55 | 0.53 | 0.88 | 23 | empty |
| 3 | 55 | 0.52 | 0.88 | 25 | empty |
| 4 | 82 | 0.43 | 0.79 | 14 | empty |
| 5 | 53 | 0.39 | 0.81 | 14 | empty |
Interfaces
4 interfaces between chains.
- B–D · 697 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 694 Ų buried · 16 hydrogen bonds · protein-protein
- A–D · 190 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 152 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 3LP9 · Crystal structure of LS24, A Seed Albumin from Lathyrus sativus · the same entry in another collection · 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
- Elsewhere: RCSB PDB 3LP9 · PDBe 3LP9
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