Research workbench
Crystal structure of a probable cytosol aminopeptidase (leucine aminopeptidase, lap) from chlamydia trachomatis D/UW-3/CX
Analyse Crystal structure of a probable cytosol aminopeptidase (leucine aminopeptidase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6OME
- Type
- protein
- Length
- 499 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable cytosol aminopeptidase
- EC
- 3.4.11.1, 3.4.11.10
- UniProt
- O84049
- Ligands
- LEU, NA, ZN, CL, CO3, SO4
- Pockets
- 4 · best druggability 0.50
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable cytosol aminopeptidase (EC 3.4.11.1, 3.4.11.10) | protein | 499 | 39% helix, 21% strand | O84049 |
Ligands and binding sites
- LEU · Leucine · ligand · chains A
- NA · Sodium ion · metal · 4 copies · chains A
- ZN · Zinc ion · metal · 2 copies · chains A
- CL · Chloride ion · ion · 2 copies · chains A
- CO3 · Carbonate ion · ion · chains A
- SO4 · Sulfate ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 226 | 0.50 | 0.75 | 37 | CO3, EDO, NA |
| 2 | 87 | 0.44 | 0.80 | 16 | empty |
| 3 | 59 | 0.33 | 0.77 | 14 | empty |
| 4 | 64 | 0.32 | 0.75 | 15 | empty |
Compared structures
- 6OME · Crystal structure of a probable cytosol aminopeptidase (Leucine aminopeptidase, LAP) from… · the same entry in another collection · chain A against A, TM-score 1.00
- O84049 · AlphaFold monomer V2.0 prediction for probable cytosol aminopeptidase (O84049) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 O84049
- Elsewhere: RCSB PDB 6OME · PDBe 6OME · UniProt O84049
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