Research workbench
Crystal structure of putative cyclophilin B from brugia malayi
Analyse Crystal structure of putative cyclophilin B from brugia malayi in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8CU5
- Type
- protein
- Length
- 549 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptidyl-prolyl cis-trans isomerase
- EC
- 5.2.1.8
- UniProt
- Q6YNZ2
- Ligands
- SO4
- Pockets
- 5 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 13% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Peptidyl-prolyl cis-trans isomerase (EC 5.2.1.8) | protein | 183 | 13% helix, 37% strand | Q6YNZ2 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, C
- EDO · 1,2-ethanediol · additive · 6 copies · chains A, B, 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 946 | 0.75 | 0.78 | 96 | EDO, SO4 |
| 2 | 88 | 0.39 | 0.77 | 21 | empty |
| 3 | 78 | 0.38 | 0.78 | 22 | EDO |
| 4 | 62 | 0.38 | 0.79 | 20 | EDO |
| 5 | 61 | 0.36 | 0.78 | 15 | SO4 |
Interfaces
2 interfaces between chains.
- A–B · 641 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 524 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 8CU5 · Crystal Structure of Putative Cyclophilin B from Brugia malayi · 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 Q6YNZ2
- Elsewhere: RCSB PDB 8CU5 · PDBe 8CU5 · UniProt Q6YNZ2
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