MolNFT v1 · #183570 · protein
Endoplasmic reticulum aminopeptidase 2 complexed with a mixed hydroxamic and sulfonyl ligand
7NUP: “Endoplasmic reticulum aminopeptidase 2 complexed with a mixed hydroxamic and sulfonyl ligand”. X-ray diffraction, 6 ligands (USK, NAG, BMA), 20 pockets (best druggability 0.84). MolNFT v1 #183570 on GenesisL1: 3D structure, binding…
- PDB
- 7NUP
- Type
- protein
- Length
- 3,589 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endoplasmic reticulum aminopeptidase 2
- EC
- 3.4.11.-
- UniProt
- Q6P179
- Ligands
- USK, NAG, BMA, MAN, ZN, BR
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 46% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Endoplasmic reticulum aminopeptidase 2 (EC 3.4.11.-) | protein | 915 | 46% helix, 21% strand | Q6P179 |
| B | Endoplasmic reticulum aminopeptidase 2 (EC 3.4.11.-) | protein | 907 | 46% helix, 21% strand | Q6P179 |
| C | Endoplasmic reticulum aminopeptidase 2 (EC 3.4.11.-) | protein | 883 | 46% helix, 21% strand | Q6P179 |
| D | Endoplasmic reticulum aminopeptidase 2 (EC 3.4.11.-) | protein | 884 | 46% helix, 20% strand | Q6P179 |
Ligands and binding sites
- USK · (3~{S})-4-(4-hydroxyphenyl)-~{N}-oxidanyl-3-[5-[[(5-phenylthiophen-2-yl)sulfonylamino]methyl]-1,2,3-triazol-1-yl]butanamide · ligand · 4 copies · chains A, B, C, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 47 copies · chains A, B, D, C
- BMA · beta-D-mannopyranose · sugar · 7 copies · chains D, B
- MAN · alpha-D-mannopyranose · sugar · 4 copies
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- BR · Bromide ion · ion · 13 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B, D
- PGE · Triethylene glycol · 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, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 760 | 0.84 | 0.87 | 78 | USK, BR |
| 2 | 860 | 0.84 | 0.86 | 92 | USK, BR |
| 3 | 811 | 0.83 | 0.85 | 104 | empty |
| 4 | 624 | 0.82 | 0.87 | 57 | USK, BR |
| 5 | 431 | 0.78 | 0.86 | 42 | USK, BR |
Interfaces
5 interfaces between chains.
- A–C · 863 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 608 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 317 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 193 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 33 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 32 glycan, 8 disulfide (N-glycosylation, disulfide).
Compared structures
- 7NUP · Endoplasmic reticulum aminopeptidase 2 complexed with a mixed hydroxamic and sulfonyl… · the same entry in another collection · chain D against D, TM-score 1.00
- Q6P179 · AlphaFold monomer V2.0 prediction for endoplasmic reticulum aminopeptidase 2 (Q6P179) · a predicted model of the same protein · chain C 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 7NUP · PDBe 7NUP · UniProt Q6P179
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