MolNFT v1 · #115790 · protein
Crystal structure of ERAP2 without catalytic ZN(II) atom
5CU5 · Endoplasmic reticulum aminopeptidase 2: “Crystal structure of ERAP2 without catalytic ZN(II) atom”. X-ray diffraction, 2 ligands (NAG, MAN), 16 pockets (best druggability 0.83). MolNFT v1 #115790 on GenesisL1: 3D structure, binding…
- PDB
- 5CU5
- Type
- protein
- Length
- 1,733 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
- NAG, MAN
- Pockets
- 16 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Endoplasmic reticulum aminopeptidase 2 (EC 3.4.11.-) | protein | 871 | 46% helix, 21% strand | Q6P179 |
| B | Endoplasmic reticulum aminopeptidase 2 (EC 3.4.11.-) | protein | 862 | 46% helix, 21% strand | Q6P179 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 17 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 3 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 608 | 0.83 | 0.88 | 81 | empty |
| 2 | 838 | 0.83 | 0.85 | 88 | empty |
| 3 | 487 | 0.78 | 0.85 | 56 | empty |
| 4 | 282 | 0.78 | 0.90 | 37 | empty |
| 5 | 279 | 0.68 | 0.83 | 54 | empty |
Interfaces
1 interface between chains.
- A–B · 670 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 13 glycan, 1 disulfide (N-glycosylation, disulfide).
Compared structures
- 5CU5 · Crystal structure of ERAP2 without catalytic Zn(II) atom · 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 B 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 5CU5 · PDBe 5CU5 · UniProt Q6P179
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