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Crystal structure of endoplasmic reticulum aminopeptidase 2 (ERAP2) complex with a highly selective and potent small molecule
Analyse Crystal structure of endoplasmic reticulum aminopeptidase 2 (ERAP2) complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7SH0
- Type
- protein
- Length
- 1,737 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
- GIY, ZN, NA
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Endoplasmic reticulum aminopeptidase 2 (EC 3.4.11.-) | protein | 896 | 47% helix, 20% strand | Q6P179 |
| B | Endoplasmic reticulum aminopeptidase 2 (EC 3.4.11.-) | protein | 841 | 47% helix, 18% strand | Q6P179 |
Ligands and binding sites
- GIY · (2S)-N-hydroxy-3-(4-methoxyphenyl)-2-[4-({[5-(pyridin-2-yl)thiophene-2-sulfonyl]amino}methyl)-1H-1,2,3-triazol-1-yl]propanamide · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- NA · Sodium ion · metal · chains A
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 4 copies · chains A, B
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 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, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 596 | 0.82 | 0.87 | 62 | GIY |
| 2 | 670 | 0.81 | 0.85 | 79 | empty |
| 3 | 507 | 0.80 | 0.87 | 52 | GIY |
| 4 | 496 | 0.73 | 0.82 | 39 | empty |
| 5 | 359 | 0.73 | 0.84 | 39 | empty |
Interfaces
1 interface between chains.
- A–B · 614 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 7SH0 · Crystal structure of endoplasmic reticulum aminopeptidase 2 (ERAP2) complex with a highly… · 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 7SH0 · PDBe 7SH0 · UniProt Q6P179
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