MolNFT v1 · #55198 · protein
Crystal structure of the soluble domain of human endoplasmic reticulum aminopeptidase 1 ERAP1
2YD0: “Crystal structure of the soluble domain of human endoplasmic reticulum aminopeptidase 1 ERAP1”. X-ray diffraction, 4 ligands (BES, NAG, K), 10 pockets (best druggability 0.83). MolNFT v1 #55198 on GenesisL1: 3D structure, binding…
- PDB
- 2YD0
- Type
- protein
- Length
- 858 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endoplasmic reticulum aminopeptidase 1
- EC
- 3.4.11.-
- UniProt
- Q9NZ08
- Ligands
- BES, NAG, K, ZN
- Pockets
- 10 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Endoplasmic reticulum aminopeptidase 1 (EC 3.4.11.-) | protein | 858 | 46% helix, 23% strand | Q9NZ08 |
Ligands and binding sites
- BES · 2-(3-amino-2-hydroxy-4-phenyl-butyrylamino)-4-methyl-pentanoic acid · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A
- K · Potassium ion · metal · 2 copies · chains A
- ZN · Zinc ion · metal · chains A
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 722 | 0.83 | 0.87 | 75 | BES |
| 2 | 272 | 0.71 | 0.85 | 41 | empty |
| 3 | 310 | 0.58 | 0.77 | 57 | K |
| 4 | 104 | 0.51 | 0.82 | 17 | empty |
| 5 | 88 | 0.50 | 0.83 | 19 | empty |
Modifications
Observed in the structure: 3 glycan, 2 disulfide (N-glycosylation, disulfide).
Compared structures
- 2YD0 · Crystal structure of the soluble domain of human endoplasmic reticulum aminopeptidase 1… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9NZ08 · AlphaFold monomer V2.0 prediction for endoplasmic reticulum aminopeptidase 1 (Q9NZ08) · 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 Q9NZ08
- Elsewhere: RCSB PDB 2YD0 · PDBe 2YD0 · UniProt Q9NZ08
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