Research workbench
Human ERAP1 bound to phosphinic pseudotripeptide inhibitor DG013
Analyse Human ERAP1 bound to phosphinic pseudotripeptide inhibitor DG013 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6M8P
- Type
- protein
- Length
- 18,942 residues
- Chains
- 22
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.31
- Source
- Homo sapiens
- Molecule
- Endoplasmic reticulum aminopeptidase 1
- EC
- 3.4.11.-
- UniProt
- Q9NZ08
- Ligands
- P52, NAG, BMA, ZN, SO4
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · resolution 3.31 · 1 distinct chain · 46% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V | Endoplasmic reticulum aminopeptidase 1 (EC 3.4.11.-) | protein | 861 | 46% helix, 22% strand | Q9NZ08 |
Ligands and binding sites
- P52 · Nalpha-[(2S)-2-{[[(1R)-1-amino-3-phenylpropyl](hydroxy)phosphoryl]methyl}-4-methylpentanoyl]-L-tryptophanamide · ligand · 22 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 110 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V
- BMA · beta-D-mannopyranose · sugar · 44 copies
- ZN · Zinc ion · metal · 22 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V
- SO4 · Sulfate ion · ion · 309 copies · chains A, G, D, B, F, H, C, J, E, L, K, I, N, Q, M, P, U, O, S, T, R, V
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 804 | 0.83 | 0.86 | 96 | P52, SO4 |
| 2 | 743 | 0.83 | 0.86 | 78 | P52, SO4 |
| 3 | 994 | 0.82 | 0.83 | 87 | P52, SO4 |
| 4 | 739 | 0.82 | 0.86 | 84 | ZN, P52, SO4 |
| 5 | 710 | 0.82 | 0.86 | 74 | P52, SO4 |
Interfaces
33 interfaces between chains.
- N–Q · 754 Ų buried · 8 hydrogen bonds · protein-protein
- I–K · 748 Ų buried · 8 hydrogen bonds · protein-protein
- M–O · 745 Ų buried · 8 hydrogen bonds · protein-protein
- P–R · 740 Ų buried · 8 hydrogen bonds · protein-protein
- D–F · 740 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 44 disulfide, 25 glycan (disulfide, N-glycosylation).
Compared structures
- Q9NZ08 · AlphaFold monomer V2.0 prediction for endoplasmic reticulum aminopeptidase 1 (Q9NZ08) · a predicted model of the same protein · chain G 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 6M8P · PDBe 6M8P · UniProt Q9NZ08
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.