MolNFT v1 · #67786 · protein
APPEP_D266NX+H2H3 opened state
3IUR · Prolyl endopeptidase: “APPEP_D266NX+H2H3 opened state”. X-ray diffraction, 7 pockets (best druggability 0.63). MolNFT v1 #67786 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3IUR
- Type
- protein
- Length
- 679 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Prolyl endopeptidase; H2H3 helices from villin headpiece subdomain HP35
- UniProt
- Q9X6R4
- Pockets
- 7 · best druggability 0.63
Structure
x-ray diffraction · 3 distinct chains · 22% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Prolyl endopeptidase | protein | 668 | 23% helix, 34% strand | Q9X6R4 |
| B | H2H3 helices from villin headpiece subdomain HP35 | protein | 6 | 0% helix, 0% strand | — |
| C | H2H3 helices from villin headpiece subdomain HP35 | protein | 5 | 0% helix, 0% strand | — |
Ligands and binding sites
- GOL · Glycerol · additive · 3 copies · chains A, C
- 15P · Polyethylene glycol (N=34) · additive · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 553 | 0.63 | 0.75 | 45 | empty |
| 2 | 245 | 0.48 | 0.73 | 32 | empty |
| 3 | 136 | 0.38 | 0.73 | 28 | empty |
| 4 | 115 | 0.38 | 0.74 | 23 | GOL |
| 5 | 72 | 0.32 | 0.75 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–B · 346 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 263 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 50 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3IUR · apPEP_D266Nx+H2H3 opened state · the same entry in another collection · 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 Q9X6R4
- Elsewhere: RCSB PDB 3IUR · PDBe 3IUR · UniProt Q9X6R4
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