MolNFT v1 · #128004 · protein
Crystal structure of a thermostabilised human protease-activated receptor-2 (PAR2) in complex with AZ8838 at 2.8 ångström resolution
5NDD · LYSOZYME,PROTEINASE-activated receptor 2,SOLUBLE cytochrome…: “Crystal structure of a thermostabilised human protease-activated receptor-2 (PAR2) in complex with AZ8838 at…”. X-ray diffraction, 3 ligands (8TZ, NA, PO4), 5 pockets…
- PDB
- 5NDD
- Type
- protein
- Length
- 567 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
- 8TZ, NA, PO4
- Pockets
- 5 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 75% helix, 4% 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 | 567 | 75% helix, 4% strand | D9IEF7, P55085, P0ABE7 |
Ligands and binding sites
- 8TZ · (~{S})-(4-fluoranyl-2-propyl-phenyl)-(1~{H}-imidazol-2-yl)methanol · ligand · chains A
- NA · Sodium ion · metal · chains A
- PO4 · Phosphate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 113 | 0.81 | 0.99 | 26 | 8TZ |
| 2 | 484 | 0.64 | 0.76 | 59 | empty |
| 3 | 172 | 0.61 | 0.83 | 29 | empty |
| 4 | 266 | 0.54 | 0.76 | 31 | empty |
| 5 | 58 | 0.26 | 0.72 | 13 | empty |
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 5NDD · 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 0.54
- 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 5NDD · PDBe 5NDD · UniProt D9IEF7 · UniProt P55085 · UniProt P0ABE7
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