Research workbench
Crystal structure of aminopeptidase ERAP2 with ligand
Analyse Crystal structure of aminopeptidase ERAP2 with ligand in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5AB0
- Type
- protein
- Length
- 1,807 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endoplasmatic reticulum aminopeptidase 2; DG025
- EC
- 3.4.11.1, 3.4.11.6
- UniProt
- Q6P179
- Ligands
- 2X0, 7GA, NAG, BMA, ZN
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 45% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Endoplasmatic reticulum aminopeptidase 2 (EC 3.4.11.1, 3.4.11.6) | protein | 910 | 46% helix, 20% strand | Q6P179 |
| C | Endoplasmatic reticulum aminopeptidase 2 (EC 3.4.11.1, 3.4.11.6) | protein | 881 | 45% helix, 20% strand | Q6P179 |
| E, F | DG025 | protein | 8 | 0% helix, 0% strand | — |
Ligands and binding sites
- 2X0 · [(1R)-1-amino-3-phenylpropyl]phosphonic acid · ligand · 2 copies · chains A, E, C, F
- 7GA · 2,4-dimethylpentanal · ligand · 2 copies · chains A, E, C, F
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 22 copies · chains A, C
- BMA · beta-D-mannopyranose · sugar · 5 copies · chains A
- ZN · Zinc ion · metal · 2 copies · chains A, C
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, C
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 251 | 0.83 | 0.96 | 46 | 2X0, 7GA |
| 2 | 269 | 0.82 | 0.93 | 48 | 2X0, 7GA |
| 3 | 1060 | 0.81 | 0.82 | 92 | empty |
| 4 | 279 | 0.80 | 0.91 | 56 | empty |
| 5 | 294 | 0.75 | 0.87 | 45 | empty |
Interfaces
3 interfaces between chains.
- A–E · 857 Ų buried · 5 hydrogen bonds · protein-protein
- C–F · 817 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 594 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 glycan, 4 disulfide, 2 covalent, 2 modified (N-glycosylation, disulfide, covalent ligand, nonstandard).
Compared structures
- 5AB0 · Crystal structure of aminopeptidase ERAP2 with ligand · 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 C 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 5AB0 · PDBe 5AB0 · UniProt Q6P179
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