MolNFT v1 · #40968 · protein
Bllap in complex with microginin FR1
2J9A · Cytosol aminopeptidase: “Bllap in complex with microginin FR1”. X-ray diffraction, 3 ligands (AHY, ZN, CL), 3 pockets (best druggability 0.55). MolNFT v1 #40968 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2J9A
- Type
- protein
- Length
- 489 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytosol aminopeptidase; Microginin FR1
- EC
- 3.4.11.1, 3.4.11.5
- UniProt
- P00727
- Ligands
- AHY, ZN, CL
- Pockets
- 3 · best druggability 0.55
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytosol aminopeptidase (EC 3.4.11.1, 3.4.11.5) | protein | 485 | 39% helix, 21% strand | P00727 |
| D | Microginin FR1 | protein | 4 | 0% helix, 0% strand | — |
Ligands and binding sites
- AHY · (2S,3R)-3-amino-2-hydroxydecanoic acid · ligand · chains A, D
- ZN · Zinc ion · metal · 2 copies · chains A, D
- CL · Chloride ion · ion · chains A, D
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 3 copies · chains A
- DMS · Dimethyl sulfoxide · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 190 | 0.55 | 0.79 | 28 | AHY |
| 2 | 130 | 0.41 | 0.75 | 20 | empty |
| 3 | 66 | 0.35 | 0.77 | 15 | empty |
Interfaces
1 interface between chains.
- A–D · 413 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent, 1 modified (covalent ligand, nonstandard).
Compared structures
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 P00727
- Elsewhere: RCSB PDB 2J9A · PDBe 2J9A · UniProt P00727
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