MolNFT v1 · #118274 · protein
Crystal structure of cyclophilin AQUACYP293 from hirschia baltica
5EX2 · Peptidyl-prolyl cis-trans isomerase: “Crystal structure of cyclophilin AQUACYP293 from hirschia baltica”. X-ray diffraction, 3 ligands (MG, CA, CL), 4 pockets (best druggability 0.67). MolNFT v1 #118274 on GenesisL1: 3D structure…
- PDB
- 5EX2
- Type
- protein
- Length
- 533 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptidyl-prolyl cis-trans isomerase
- EC
- 5.2.1.8
- UniProt
- C6XJ17
- Ligands
- MG, CA, CL
- Pockets
- 4 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 21% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peptidyl-prolyl cis-trans isomerase (EC 5.2.1.8) | protein | 267 | 21% helix, 30% strand | C6XJ17 |
| B | Peptidyl-prolyl cis-trans isomerase (EC 5.2.1.8) | protein | 266 | 21% helix, 30% strand | C6XJ17 |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A
- CA · Calcium ion · metal · chains B
- CL · Chloride ion · ion · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 666 | 0.67 | 0.76 | 57 | empty |
| 2 | 159 | 0.48 | 0.77 | 29 | empty |
| 3 | 130 | 0.45 | 0.77 | 19 | empty |
| 4 | 114 | 0.41 | 0.76 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 231 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5EX2 · Crystal structure of cyclophilin AquaCyp293 from Hirschia baltica · 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 C6XJ17
- Elsewhere: RCSB PDB 5EX2 · PDBe 5EX2 · UniProt C6XJ17
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