Research workbench
Crystal structure of the peptidylprolyl isomerase domain of human PPWD1
Analyse Crystal structure of the peptidylprolyl isomerase domain of human PPWD1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2A2N
- Type
- protein
- Length
- 493 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptidylprolyl isomerase domain and wd repeat containing 1
- EC
- 5.2.1.8
- UniProt
- Q96BP3
- Pockets
- 5 · best druggability 0.57
Structure
x-ray diffraction · 2 distinct chains · 14% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Peptidylprolyl isomerase domain and wd repeat containing 1 (EC 5.2.1.8) | protein | 164 | 14% helix, 29% strand | Q96BP3 |
| C | Peptidylprolyl isomerase domain and wd repeat containing 1 (EC 5.2.1.8) | protein | 165 | 15% helix, 31% strand | Q96BP3 |
Ligands and binding sites
- GOL · Glycerol · additive · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 307 | 0.57 | 0.76 | 36 | empty |
| 2 | 289 | 0.55 | 0.76 | 39 | empty |
| 3 | 107 | 0.38 | 0.75 | 22 | empty |
| 4 | 109 | 0.36 | 0.74 | 22 | empty |
| 5 | 74 | 0.32 | 0.75 | 23 | empty |
Interfaces
2 interfaces between chains.
- A–C · 611 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 603 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 2A2N · Crystal Structure of the peptidylprolyl isomerase domain of Human PPWD1 · the same entry in another collection · chain A against A, TM-score 1.00
- Q96BP3 · AlphaFold monomer V2.0 prediction for peptidylprolyl isomerase domain and wd… · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q96BP3
- Elsewhere: RCSB PDB 2A2N · PDBe 2A2N · UniProt Q96BP3
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