Research workbench
Crystal structure of the peptidylprolyl isomerase domain of arabidopsis thaliana CYP71.
Analyse Crystal structure of the peptidylprolyl isomerase domain of arabidopsis… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6LKB
- Type
- protein
- Length
- 320 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptidyl-prolyl cis-trans isomerase CYP71
- EC
- 5.2.1.8
- UniProt
- Q8W4D0
- Ligands
- CO, PO4, SO4
- Pockets
- 3 · best druggability 0.33
Structure
x-ray diffraction · 1 distinct chain · 14% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Peptidyl-prolyl cis-trans isomerase CYP71 (EC 5.2.1.8) | protein | 160 | 14% helix, 30% strand | Q8W4D0 |
Ligands and binding sites
- CO · Cobalt (II) ion · metal · 3 copies · chains A, B
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · chains B
- GOL · Glycerol · additive · 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 | 65 | 0.33 | 0.76 | 25 | empty |
| 2 | 51 | 0.29 | 0.76 | 17 | empty |
| 3 | 51 | 0.26 | 0.74 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 322 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 6LKB · Crystal Structure of the peptidylprolyl isomerase domain of Arabidopsis thaliana CYP71. · the same entry in another collection · chain A against A, TM-score 1.00
- Q8W4D0 · AlphaFold monomer V2.0 prediction for peptidyl-prolyl cis-trans isomerase CYP71 (Q8W4D0) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q8W4D0
- Elsewhere: RCSB PDB 6LKB · PDBe 6LKB · UniProt Q8W4D0
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