MolNFT v1 · #96163 · protein
Crystal structure of the human endoplasmic reticulum aminopeptidase 2 in complex with phosphinic pseudotripeptide inhibitor.
4JBS: “Crystal structure of the human endoplasmic reticulum aminopeptidase 2 in complex with phosphinic…”. X-ray diffraction, 4 ligands (P52, NAG, MAN), 20 pockets (best druggability 0.78). MolNFT v1 #96163 on GenesisL1: 3D structure…
- PDB
- 4JBS
- Type
- protein
- Length
- 1,723 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endoplasmic reticulum aminopeptidase 2
- EC
- 3.4.11.-
- UniProt
- Q6P179
- Ligands
- P52, NAG, MAN, ZN
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Endoplasmic reticulum aminopeptidase 2 (EC 3.4.11.-) | protein | 869 | 45% helix, 20% strand | Q6P179 |
| B | Endoplasmic reticulum aminopeptidase 2 (EC 3.4.11.-) | protein | 854 | 44% helix, 17% strand | Q6P179 |
Ligands and binding sites
- P52 · Nalpha-[(2S)-2-{[[(1R)-1-amino-3-phenylpropyl](hydroxy)phosphoryl]methyl}-4-methylpentanoyl]-L-tryptophanamide · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 13 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 2 copies · chains A
- ZN · Zinc ion · metal · 2 copies · chains A, B
- IMD · Imidazole · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 337 | 0.78 | 0.88 | 44 | P52 |
| 2 | 432 | 0.77 | 0.86 | 41 | P52 |
| 3 | 450 | 0.74 | 0.83 | 52 | IMD |
| 4 | 412 | 0.74 | 0.84 | 41 | empty |
| 5 | 206 | 0.73 | 0.89 | 38 | empty |
Interfaces
1 interface between chains.
- A–B · 592 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 glycan, 4 disulfide (N-glycosylation, disulfide).
Compared structures
- 4JBS · Crystal structure of the human Endoplasmic Reticulum Aminopeptidase 2 in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
- Q6P179 · AlphaFold monomer V2.0 prediction for endoplasmic reticulum aminopeptidase 2 (Q6P179) · a predicted model of the same protein · 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
- Every structure of UniProt Q6P179
- Elsewhere: RCSB PDB 4JBS · PDBe 4JBS · UniProt Q6P179
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.