Research workbench
Er aminopeptidase, ERAP1, bound to the zinc aminopeptidase inhibitor, bestatin
Analyse Er aminopeptidase, ERAP1, bound to the zinc aminopeptidase inhibitor, bestatin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3MDJ
- Type
- protein
- Length
- 2,458 residues
- Chains
- 3
- 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, MAN, BMA, ZN
- Pockets
- 20 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 43% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Endoplasmic reticulum aminopeptidase 1 (EC 3.4.11.-) | protein | 818 | 43% helix, 23% strand | Q9NZ08 |
| B | Endoplasmic reticulum aminopeptidase 1 (EC 3.4.11.-) | protein | 821 | 44% helix, 22% strand | Q9NZ08 |
| C | Endoplasmic reticulum aminopeptidase 1 (EC 3.4.11.-) | protein | 819 | 43% helix, 23% strand | Q9NZ08 |
Ligands and binding sites
- BES · 2-(3-amino-2-hydroxy-4-phenyl-butyrylamino)-4-methyl-pentanoic acid · ligand · 3 copies · chains A, B, C
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 9 copies · chains A, B, C
- MAN · alpha-D-mannopyranose · sugar · 4 copies · chains A, C
- BMA · beta-D-mannopyranose · sugar · 2 copies
- ZN · Zinc ion · metal · 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, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 944 | 0.73 | 0.76 | 75 | BES |
| 2 | 811 | 0.72 | 0.77 | 66 | empty |
| 3 | 904 | 0.72 | 0.76 | 106 | empty |
| 4 | 956 | 0.71 | 0.75 | 93 | empty |
| 5 | 826 | 0.70 | 0.76 | 79 | empty |
Interfaces
3 interfaces between chains.
- B–C · 528 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 522 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 468 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- 3MDJ · ER Aminopeptidase, ERAP1, Bound to the Zinc Aminopeptidase Inhibitor, Bestatin · 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 B against A, TM-score 0.85
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 3MDJ · PDBe 3MDJ · UniProt Q9NZ08
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