Research workbench
Tomato leucine aminopeptidase mutant - K354E
Analyse Tomato leucine aminopeptidase mutant - K354E in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5D8N
- Type
- protein
- Length
- 1,513 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Leucine aminopeptidase 1, chloroplastic
- EC
- 3.4.11.1, 3.4.11.5
- UniProt
- Q10712
- Ligands
- MG, CL
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Leucine aminopeptidase 1, chloroplastic (EC 3.4.11.1, 3.4.11.5) | protein | 505 | 37% helix, 22% strand | Q10712 |
| B, C | Leucine aminopeptidase 1, chloroplastic (EC 3.4.11.1, 3.4.11.5) | protein | 504 | 38% helix, 22% strand | Q10712 |
Ligands and binding sites
- MG · Magnesium ion · metal · 7 copies · chains A, B, C
- CL · Chloride ion · ion · 8 copies · chains A, C, B
- EDO · 1,2-ethanediol · additive · 7 copies · chains B, A, C
- ACT · Acetate ion · additive · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 823 | 0.79 | 0.82 | 83 | empty |
| 2 | 676 | 0.73 | 0.80 | 65 | empty |
| 3 | 449 | 0.72 | 0.82 | 51 | empty |
| 4 | 66 | 0.70 | 0.96 | 21 | MG |
| 5 | 360 | 0.67 | 0.80 | 58 | EDO |
Interfaces
3 interfaces between chains.
- B–C · 1095 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 936 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 594 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- Q10712 · AlphaFold monomer V2.0 prediction for leucine aminopeptidase 1, chloroplastic (Q10712) · a predicted model of the same protein · chain B 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 Q10712
- Elsewhere: RCSB PDB 5D8N · PDBe 5D8N · UniProt Q10712
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