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Crystal structure of toxoplasma gondii peptidyl-prolyl cis-trans isomerase, 541.M00136
Analyse Crystal structure of toxoplasma gondii peptidyl-prolyl cis-trans isomerase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3BO7
- Type
- protein
- Length
- 713 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptidyl-prolyl cis-trans isomerase cyclophilin-type; Cyclosporin a
- UniProt
- D0VWS5
- Ligands
- SO4
- Pockets
- 2 · best druggability 0.76
Structure
x-ray diffraction · 5 distinct chains · 15% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peptidyl-prolyl cis-trans isomerase cyclophilin-type | protein | 165 | 15% helix, 32% strand | D0VWS5 |
| B | Peptidyl-prolyl cis-trans isomerase cyclophilin-type | protein | 167 | 14% helix, 32% strand | D0VWS5 |
| C | Peptidyl-prolyl cis-trans isomerase cyclophilin-type | protein | 169 | 15% helix, 30% strand | D0VWS5 |
| D | Peptidyl-prolyl cis-trans isomerase cyclophilin-type | protein | 168 | 15% helix, 31% strand | D0VWS5 |
| E, F, G, H | Cyclosporin a | protein | 11 | 0% helix, 0% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 22 copies · chains A, C, D, B, H, E
- EDO · 1,2-ethanediol · additive · 7 copies · chains A, C, D, H, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 974 | 0.76 | 0.78 | 90 | SO4 |
| 2 | 438 | 0.70 | 0.81 | 36 | SO4, EDO |
Interfaces
15 interfaces between chains.
- C–G · 490 Ų buried · 9 hydrogen bonds · protein-protein
- B–F · 487 Ų buried · 9 hydrogen bonds · protein-protein
- A–E · 476 Ų buried · 8 hydrogen bonds · protein-protein
- D–H · 476 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 374 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 32 modified, 4 d-amino (nonstandard, methylation, D-amino acid).
Compared structures
- 3BO7 · Crystal structure of Toxoplasma gondii peptidyl-prolyl cis-trans isomerase, 541.m00136 · 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 D0VWS5
- Elsewhere: RCSB PDB 3BO7 · PDBe 3BO7 · UniProt D0VWS5
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