MolNFT v1 · #29818 · protein
Crystal structure of the CYCLOPHILN_RING domain of human peptidylprolyl isomerase (cyclophilin)-like 2 isoform B
1ZKC · Peptidyl-prolyl cis-trans isomerase like 2: “Crystal structure of the CYCLOPHILN_RING domain of human peptidylprolyl isomerase (cyclophilin)-like 2…”. X-ray diffraction, 3 pockets (best druggability 0.36). MolNFT v1 #29818 on…
- PDB
- 1ZKC
- Type
- protein
- Length
- 372 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptidyl-prolyl cis-trans isomerase like 2
- EC
- 5.2.1.8
- UniProt
- Q13356
- Pockets
- 3 · best druggability 0.36
Structure
x-ray diffraction · 2 distinct chains · 22% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peptidyl-prolyl cis-trans isomerase like 2 (EC 5.2.1.8) | protein | 187 | 22% helix, 29% strand | Q13356 |
| B | Peptidyl-prolyl cis-trans isomerase like 2 (EC 5.2.1.8) | protein | 185 | 22% helix, 30% strand | Q13356 |
Ligands and binding sites
- BME · Beta-mercaptoethanol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 95 | 0.36 | 0.75 | 19 | empty |
| 2 | 81 | 0.35 | 0.75 | 20 | empty |
| 3 | 67 | 0.32 | 0.75 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 425 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 1 disulfide (additive adduct, disulfide).
Compared structures
- 1ZKC · Crystal Structure of the cyclophiln_RING domain of human peptidylprolyl isomerase… · the same entry in another collection · chain A against A, TM-score 1.00
- Q13356 · AlphaFold monomer V2.0 prediction for ring-type E3 ubiquitin-protein ligase PPIL2 (Q13356) · a predicted model of the same protein · chain A against A, TM-score 0.93
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 Q13356
- Elsewhere: RCSB PDB 1ZKC · PDBe 1ZKC · UniProt Q13356
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.