MolNFT v1 · #123007 · protein
Crystal structure of endoplasmic reticulum aminopeptidase 2 (ERAP2) in complex with a hydroxamic derivative ligand
5J6S: “Crystal structure of endoplasmic reticulum aminopeptidase 2 (ERAP2) in complex with a hydroxamic derivative…”. X-ray diffraction, 5 ligands (6GA, NAG, BMA), 20 pockets (best druggability 0.82). MolNFT v1 #123007 on GenesisL1: 3D…
- PDB
- 5J6S
- Type
- protein
- Length
- 1,790 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
- 6GA, NAG, BMA, MAN, ZN
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Endoplasmic reticulum aminopeptidase 2 (EC 3.4.11.-) | protein | 910 | 46% helix, 19% strand | Q6P179 |
| B | Endoplasmic reticulum aminopeptidase 2 (EC 3.4.11.-) | protein | 880 | 43% helix, 18% strand | Q6P179 |
Ligands and binding sites
- 6GA · (2S)-N~1~-benzyl-2-[(4-fluorophenyl)methyl]-N~3~-hydroxypropanediamide · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 21 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 3 copies · chains A
- MAN · alpha-D-mannopyranose · sugar · 2 copies · chains A
- ZN · Zinc ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 510 | 0.82 | 0.88 | 82 | empty |
| 2 | 356 | 0.78 | 0.88 | 39 | 6GA |
| 3 | 295 | 0.78 | 0.89 | 37 | 6GA |
| 4 | 430 | 0.74 | 0.84 | 61 | empty |
| 5 | 364 | 0.73 | 0.85 | 60 | empty |
Interfaces
1 interface between chains.
- A–B · 612 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 glycan, 5 disulfide (N-glycosylation, disulfide).
Compared structures
- 5J6S · Crystal structure of Endoplasmic Reticulum Aminopeptidase 2 (ERAP2) in complex with a… · 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 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 Q6P179
- Elsewhere: RCSB PDB 5J6S · PDBe 5J6S · UniProt Q6P179
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