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Crystal structure of cyclophilin B in complex with calmegin fragment
Analyse Crystal structure of cyclophilin B in complex with calmegin fragment in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ICI
- Type
- protein
- Length
- 382 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptidyl-prolyl cis-trans isomerase B; Calnexin
- EC
- 5.2.1.8
- UniProt
- P23284
- Ligands
- ZN
- Pockets
- 2 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 14% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peptidyl-prolyl cis-trans isomerase B (EC 5.2.1.8) | protein | 187 | 15% helix, 36% strand | P23284 |
| B | Peptidyl-prolyl cis-trans isomerase B (EC 5.2.1.8) | protein | 186 | 12% helix, 36% strand | P23284 |
| C | Calnexin | protein | 9 | 44% helix, 0% strand | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, B
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 640 | 0.69 | 0.77 | 57 | empty |
| 2 | 66 | 0.35 | 0.77 | 19 | empty |
Interfaces
2 interfaces between chains.
- A–C · 456 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 242 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 3ICI · Crystal structure of cyclophilin B in complex with calmegin fragment · the same entry in another collection · chain A against A, TM-score 1.00
- P23284 · AlphaFold monomer V2.0 prediction for peptidyl-prolyl cis-trans isomerase B (P23284) · a predicted model of the same protein · chain B 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 P23284
- Elsewhere: RCSB PDB 3ICI · PDBe 3ICI · UniProt P23284
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