MolNFT v1 · #107059 · protein
Ppiase in complex with a non-phosphate small molecule inhibitor.
4TYO · Peptidyl-prolyl cis-trans isomerase nima-interacting 1: “Ppiase in complex with a non-phosphate small molecule inhibitor.”. X-ray diffraction, 1 ligand (39X), 3 pockets (best druggability 0.35). MolNFT v1 #107059 on GenesisL1: 3D…
- PDB
- 4TYO
- Type
- protein
- Length
- 228 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptidyl-prolyl cis-trans isomerase nima-interacting 1
- EC
- 5.2.1.8
- UniProt
- Q13526
- Ligands
- 39X
- Pockets
- 3 · best druggability 0.35
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peptidyl-prolyl cis-trans isomerase nima-interacting 1 (EC 5.2.1.8) | protein | 113 | 35% helix, 25% strand | Q13526 |
| B | Peptidyl-prolyl cis-trans isomerase nima-interacting 1 (EC 5.2.1.8) | protein | 115 | 32% helix, 19% strand | Q13526 |
Ligands and binding sites
- 39X · 3-(6-fluoro-1H-benzimidazol-2-yl)-N-(naphthalen-2-ylcarbonyl)-D-alanine · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 82 | 0.35 | 0.75 | 15 | 39X |
| 2 | 81 | 0.34 | 0.74 | 15 | 39X |
| 3 | 56 | 0.25 | 0.73 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 96 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 4TYO · PPIase in complex with a non-phosphate small molecule inhibitor. · 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 Q13526
- Elsewhere: RCSB PDB 4TYO · PDBe 4TYO · UniProt Q13526
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