MolNFT v1 · #163284 · protein
High-resolution crystal structure of ERAP1 in complex with 15MER phosphinic peptide
6RYF · Endoplasmic reticulum aminopeptidase 1: “High-resolution crystal structure of ERAP1 in complex with 15MER phosphinic peptide”. X-ray diffraction, 4 ligands (KF2, NAG, NA), 8 pockets (best druggability 0.83). MolNFT v1 #163284 on…
- PDB
- 6RYF
- Type
- protein
- Length
- 865 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endoplasmic reticulum aminopeptidase 1; Pse-arg-ile-gln-arg-ala-phe-val-thr-ile
- EC
- 3.4.11.-
- UniProt
- Q9NZ08
- Ligands
- KF2, NAG, NA, ZN
- Pockets
- 8 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Endoplasmic reticulum aminopeptidase 1 (EC 3.4.11.-) | protein | 856 | 46% helix, 22% strand | Q9NZ08 |
| G | Pse-arg-ile-gln-arg-ala-phe-val-thr-ile | protein | 9 | 0% helix, 0% strand | — |
Ligands and binding sites
- KF2 · [(1~{R})-1-azanyl-3-phenyl-propyl]-[(2~{S})-2-methanoyl-4-methyl-pentyl]phosphinic acid · ligand · chains A, G
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A
- NA · Sodium ion · metal · 4 copies · chains A
- ZN · Zinc ion · metal · chains A
- EDO · 1,2-ethanediol · additive · 21 copies · chains A, G
- B3P · 2-[3-(2-hydroxy-1,1-dihydroxymethyl-ethylamino)-propylamino]-2-hydroxymethyl-propane-1,3-diol · additive · chains A, G
- PPI · Propanoic acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 343 | 0.83 | 0.93 | 48 | B3P, EDO |
| 2 | 306 | 0.83 | 0.93 | 51 | KF2 |
| 3 | 51 | 0.60 | 0.93 | 17 | empty |
| 4 | 295 | 0.56 | 0.76 | 51 | EDO, NA |
| 5 | 80 | 0.50 | 0.83 | 18 | empty |
Interfaces
1 interface between chains.
- A–G · 984 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 glycan, 2 disulfide, 1 covalent (N-glycosylation, disulfide, covalent ligand).
Compared structures
- 6RYF · High-resolution crystal structure of ERAP1 in complex with 15mer phosphinic peptide · 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 6RYF · PDBe 6RYF · UniProt Q9NZ08
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