Research workbench
Crystal structure of ERAP2 aminopeptidase in complex with phosphinic PSEUDOTRIPEPTIDE((1R)-1-amino-3-PHENYLPROPYL){(2S)-3-[((2S)-1-amino- 1-oxo-3-phenylpropan-2-YL)AMINO]-2-{[3-(2-hydroxyphenyl)-isoxazol-5- YL]METHYL}-3-OXOPROPYL}PHOSPHINIC acid
Analyse Crystal structure of ERAP2 aminopeptidase in complex with phosphinic… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7P7P
- Type
- protein
- Length
- 1,782 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
- 62S, NAG, BMA, MAN, ZN
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Endoplasmic reticulum aminopeptidase 2 (EC 3.4.11.-) | protein | 911 | 46% helix, 20% strand | Q6P179 |
| B | Endoplasmic reticulum aminopeptidase 2 (EC 3.4.11.-) | protein | 871 | 42% helix, 19% strand | Q6P179 |
Ligands and binding sites
- 62S · [(2~{S})-3-[[(2~{S})-1-azanyl-1-oxidanylidene-3-phenyl-propan-2-yl]amino]-2-[[3-(2-hydroxyphenyl)-1,2-oxazol-5-yl]methyl]-3-oxidanylidene-propyl]-[(1~{R})-1-azanyl-3-phenyl-propyl]phosphinic acid · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 24 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 4 copies · chains B, A
- MAN · alpha-D-mannopyranose · sugar · 4 copies · chains A
- ZN · Zinc ion · metal · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 7 copies · chains A
- PEG · Di(hydroxyethyl)ether · additive · 2 copies
- PDO · 1,3-propandiol · additive · 2 copies · chains A, B
- PGE · Triethylene glycol · additive · chains A
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains A
- IMD · Imidazole · additive · chains A
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 | 902 | 0.82 | 0.84 | 91 | 62S |
| 2 | 654 | 0.81 | 0.86 | 82 | EDO |
| 3 | 463 | 0.78 | 0.86 | 43 | 62S, EDO |
| 4 | 638 | 0.77 | 0.83 | 56 | empty |
| 5 | 505 | 0.77 | 0.84 | 59 | empty |
Interfaces
1 interface between chains.
- A–B · 650 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 17 glycan, 4 disulfide (N-glycosylation, disulfide).
Compared structures
- 7P7P · Crystal structure of ERAP2 aminopeptidase in complex with phosphinic… · 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 0.99
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 7P7P · PDBe 7P7P · UniProt Q6P179
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