MolNFT v1 · #123995 · protein
Crystal structure of endoplasmic reticulum aminopeptidase 2 (ERAP2) in complex with a diaminobenzoic acid derivative ligand.
5K1V: “Crystal structure of endoplasmic reticulum aminopeptidase 2 (ERAP2) in complex with a diaminobenzoic acid…”. X-ray diffraction, 4 ligands (6PX, NAG, MAN), 20 pockets (best druggability 0.83). MolNFT v1 #123995 on GenesisL1: 3D…
- PDB
- 5K1V
- Type
- protein
- Length
- 1,748 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endoplasmic reticulum aminopeptidase 2
- EC
- 3.4.11.-
- UniProt
- Q6P179
- Ligands
- 6PX, NAG, MAN, ZN
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Endoplasmic reticulum aminopeptidase 2 (EC 3.4.11.-) | protein | 899 | 47% helix, 20% strand | Q6P179 |
| B | Endoplasmic reticulum aminopeptidase 2 (EC 3.4.11.-) | protein | 849 | 46% helix, 15% strand | Q6P179 |
Ligands and binding sites
- 6PX · methyl N-[4-amino-3-(L-arginylamino)benzene-1-carbonyl]-L-tyrosinate · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 18 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 2 copies · chains A
- ZN · Zinc ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 567 | 0.83 | 0.88 | 79 | empty |
| 2 | 435 | 0.79 | 0.87 | 46 | empty |
| 3 | 692 | 0.78 | 0.83 | 54 | empty |
| 4 | 333 | 0.77 | 0.88 | 39 | 6PX |
| 5 | 352 | 0.72 | 0.84 | 38 | empty |
Interfaces
1 interface between chains.
- A–B · 658 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 glycan, 4 disulfide (N-glycosylation, disulfide).
Compared structures
- 5K1V · Crystal structure of Endoplasmic Reticulum aminopeptidase 2 (ERAP2) in complex with a… · the same entry in another collection · chain A against A, TM-score 1.00
- Q6P179 · AlphaFold monomer V2.0 prediction for endoplasmic reticulum aminopeptidase 2 (Q6P179) · a predicted model of the same protein · chain B 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 Q6P179
- Elsewhere: RCSB PDB 5K1V · PDBe 5K1V · UniProt Q6P179
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