Research workbench
ERAP1 in the open conformation bound to 10MER phosphinic inhibitor DG014
Analyse ERAP1 in the open conformation bound to 10MER phosphinic inhibitor DG014 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6MGQ
- Type
- protein
- Length
- 2,571 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endoplasmic reticulum aminopeptidase 1; Phosphinic inhibitor DG014
- EC
- 3.4.11.-
- UniProt
- Q9NZ08
- Ligands
- 2X0, 7GA, NAG, BMA, MAN, ZN, UNX
- Pockets
- 20 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 44% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Endoplasmic reticulum aminopeptidase 1 (EC 3.4.11.-) | protein | 861 | 44% helix, 22% strand | Q9NZ08 |
| B | Endoplasmic reticulum aminopeptidase 1 (EC 3.4.11.-) | protein | 858 | 46% helix, 21% strand | Q9NZ08 |
| C | Endoplasmic reticulum aminopeptidase 1 (EC 3.4.11.-) | protein | 843 | 43% helix, 21% strand | Q9NZ08 |
| D, E, F | Phosphinic inhibitor DG014 | protein | 3 | 0% helix, 0% strand | — |
Ligands and binding sites
- 2X0 · [(1R)-1-amino-3-phenylpropyl]phosphonic acid · ligand · 3 copies · chains A, D, B, E, C, F
- 7GA · 2,4-dimethylpentanal · ligand · 3 copies · chains A, D, B, E, C, F
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 12 copies · chains A, B, C
- BMA · beta-D-mannopyranose · sugar · 3 copies · chains A
- MAN · alpha-D-mannopyranose · sugar · chains A
- ZN · Zinc ion · metal · 3 copies · chains A, B, C
- UNX · Unknown atom or ion · ion · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 706 | 0.74 | 0.80 | 69 | empty |
| 2 | 610 | 0.69 | 0.78 | 73 | empty |
| 3 | 349 | 0.69 | 0.82 | 43 | empty |
| 4 | 551 | 0.69 | 0.79 | 64 | empty |
| 5 | 369 | 0.67 | 0.80 | 44 | empty |
Interfaces
6 interfaces between chains.
- A–C · 582 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 523 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 515 Ų buried · 7 hydrogen bonds · protein-protein
- C–F · 339 Ų buried · 2 hydrogen bonds · protein-protein
- B–E · 323 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 glycan, 3 covalent, 3 disulfide (N-glycosylation, covalent ligand, disulfide).
Compared structures
- 6MGQ · ERAP1 in the open conformation bound to 10mer phosphinic inhibitor DG014 · the same entry in another collection · chain F against F, TM-score 1.00
- Q9NZ08 · AlphaFold monomer V2.0 prediction for endoplasmic reticulum aminopeptidase 1 (Q9NZ08) · a predicted model of the same protein · chain B against A, TM-score 0.86
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 6MGQ · PDBe 6MGQ · UniProt Q9NZ08
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