Download MendeleyHuman Cyclophilin D Complexed with Inhibitor
Zacharchenko, T., Lian, L.Y.To be published.
6Y3E
Scaffold-ligand complex with ligand unmodelled
- PDB DOI: https://doi.org/10.2210/pdb6Y3E/pdb
- Entry: 6Y3E supersedes: 5NWO
- Classification: ISOMERASE
- Organism(s): Homo sapiens
- Expression System: Homo sapiens
- Mutation(s): No
- Deposited: 2020-02-18 Released: 2020-03-04
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.45 Å
- R-Value Free: 0.234
- R-Value Work: 0.195
- R-Value Observed: 0.197
wwPDB Validation 3D Report Full Report
This is version 1.1 of the entry. See complete history.
Literature
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Peptidyl-prolyl cis-trans isomerase F, mitochondrial | 165 | Homo sapiens | Mutation(s): 0 Gene Names: PPIF, CYP3 EC: 5.2.1.8 |  | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P30405 (Homo sapiens) Explore P30405 Go to UniProtKB: P30405 | |||||
PHAROS: P30405 GTEx: ENSG00000108179 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P30405 | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 4 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| 12P Query on 12P | G [auth A], H [auth A] | DODECAETHYLENE GLYCOL C24 H50 O13 WRZXKWFJEFFURH-UHFFFAOYSA-N |  | ||
| PO4 Query on PO4 | I [auth A] | PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K |  | ||
| EDO Query on EDO | B [auth A], C [auth A], D [auth A], E [auth A], F [auth A] | 1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N |  | ||
| NA Query on NA | J [auth A], K [auth A], L [auth A] | SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.45 Å
- R-Value Free: 0.234
- R-Value Work: 0.195
- R-Value Observed: 0.197
- Space Group: P 43 21 2
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 57.45 | α = 90 |
| b = 57.45 | β = 90 |
| c = 114.91 | γ = 90 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| PDB_EXTRACT | data extraction |
| MOSFLM | data reduction |
| SCALA | data scaling |
| PHASER | phasing |
Entry History
Deposition Data
- Released Date: 2020-03-04 Deposition Author(s): Zacharchenko, T., Lian, L.Y.
- This entry supersedes: 5NWO
Revision History (Full details and data files)
- Version 1.0: 2020-03-04
Type: Initial release - Version 1.1: 2024-01-24
Changes: Data collection, Database references, Derived calculations, Refinement description
