Research workbench
Crystal structure of peptidylprolyl isomerase from naegleria fowleri with bound FK506
Analyse Crystal structure of peptidylprolyl isomerase from naegleria fowleri with bound… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6MKE
- Type
- protein
- Length
- 468 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptidylprolyl isomerase
- EC
- 5.2.1.8
- UniProt
- A0A2H4A315
- Ligands
- FK5
- Pockets
- 6 · best druggability 0.59
Structure
x-ray diffraction · 1 distinct chain · 13% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Peptidylprolyl isomerase (EC 5.2.1.8) | protein | 117 | 13% helix, 38% strand | A0A2H4A315 |
Ligands and binding sites
- FK5 · 8-deethyl-8-[but-3-enyl]-ascomycin · ligand · 4 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 117 | 0.59 | 0.85 | 23 | empty |
| 2 | 155 | 0.47 | 0.75 | 17 | FK5 |
| 3 | 138 | 0.45 | 0.76 | 17 | FK5 |
| 4 | 94 | 0.40 | 0.76 | 14 | FK5 |
| 5 | 81 | 0.40 | 0.77 | 15 | FK5 |
Interfaces
5 interfaces between chains.
- A–B · 666 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 149 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 146 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 26 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 22 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6MKE · Crystal Structure of Peptidylprolyl Isomerase from Naegleria fowleri with bound FK506 · 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 A0A2H4A315
- Elsewhere: RCSB PDB 6MKE · PDBe 6MKE · UniProt A0A2H4A315
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