Research workbench
Crystal structure of a thermostabilised human protease-activated receptor-2 (PAR2) in complex with AZ3451 at 3.6 ångström resolution
Analyse Crystal structure of a thermostabilised human protease-activated receptor-2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5NDZ
- Type
- protein
- Length
- 556 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- LYSOZYME,PROTEINASE-activated receptor 2,SOLUBLE cytochrome B562,PROTEINASE-activated…
- EC
- 3.2.1.17
- UniProt
- D9IEF7, P55085, P0ABE7
- Ligands
- 8UN, NA
- Pockets
- 9 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 75% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | LYSOZYME,PROTEINASE-activated receptor 2,SOLUBLE cytochrome B562,PROTEINASE-activated receptor 2 (EC 3.2.1.17) | protein | 556 | 75% helix, 3% strand | D9IEF7, P55085, P0ABE7 |
Ligands and binding sites
- 8UN · 2-(6-bromanyl-1,3-benzodioxol-5-yl)-~{N}-(4-cyanophenyl)-1-[(1~{S})-1-cyclohexylethyl]benzimidazole-5-carboxamide · ligand · chains A
- NA · Sodium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 109 | 0.80 | 0.99 | 27 | empty |
| 2 | 361 | 0.62 | 0.78 | 44 | empty |
| 3 | 145 | 0.54 | 0.81 | 25 | empty |
| 4 | 148 | 0.39 | 0.73 | 25 | empty |
| 5 | 53 | 0.39 | 0.81 | 14 | empty |
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 5NDZ · Crystal structure of a thermostabilised human protease-activated receptor-2 (PAR2) in… · the same entry in another collection · chain A against A, TM-score 1.00
- P55085 · AlphaFold monomer V2.0 prediction for proteinase-activated receptor 2 (P55085) · a predicted model of the same protein · chain A against A, TM-score 0.55
- P0ABE7 · AlphaFold monomer V2.0 prediction for soluble cytochrome B562 (P0ABE7) · a predicted model of the same protein · chain A against A, TM-score 0.20
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 D9IEF7
- Every structure of UniProt P55085
- Every structure of UniProt P0ABE7
- Elsewhere: RCSB PDB 5NDZ · PDBe 5NDZ · UniProt D9IEF7 · UniProt P55085 · UniProt P0ABE7
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