MolNFT v1 · #113291 · protein
Crystal structure of aminopeptidase ERAP2 with ligand
5AB2 · Endoplasmic reticulum aminopeptidase 2: “Crystal structure of aminopeptidase ERAP2 with ligand”. X-ray diffraction, 3 ligands (NAG, BMA, ZN), 20 pockets (best druggability 0.83). MolNFT v1 #113291 on GenesisL1: 3D structure, binding…
- PDB
- 5AB2
- Type
- protein
- Length
- 1,786 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endoplasmic reticulum aminopeptidase 2; Gpi
- EC
- 3.4.11.-
- UniProt
- Q6P179
- Ligands
- NAG, BMA, ZN
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 43% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Endoplasmic reticulum aminopeptidase 2 (EC 3.4.11.-) | protein | 896 | 46% helix, 20% strand | Q6P179 |
| B | Endoplasmic reticulum aminopeptidase 2 (EC 3.4.11.-) | protein | 878 | 40% helix, 18% strand | Q6P179 |
| C, D | Gpi | protein | 6 | 0% helix, 0% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 25 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 4 copies · chains B, A
- ZN · Zinc ion · metal · 2 copies · chains A, C, B, D
- EDO · 1,2-ethanediol · additive · 6 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, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 497 | 0.83 | 0.90 | 79 | empty |
| 2 | 243 | 0.81 | 0.94 | 35 | empty |
| 3 | 223 | 0.75 | 0.90 | 36 | empty |
| 4 | 340 | 0.75 | 0.86 | 42 | empty |
| 5 | 231 | 0.74 | 0.89 | 52 | empty |
Interfaces
3 interfaces between chains.
- A–C · 585 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 582 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 553 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 glycan, 4 disulfide (N-glycosylation, disulfide).
Compared structures
- 5AB2 · Crystal structure of aminopeptidase ERAP2 with ligand · 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 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 Q6P179
- Elsewhere: RCSB PDB 5AB2 · PDBe 5AB2 · UniProt Q6P179
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