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5ZPU
LFS829 in complex with CRM1-Ran-RanBP1
- PDB DOI: https://doi.org/10.2210/pdb5ZPU/pdb
- Classification: TRANSPORT PROTEIN
- Organism(s): Homo sapiens, Saccharomyces cerevisiae S288C
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): Yes
- Deposited: 2018-04-16 Released: 2019-04-17
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.60 Å
- R-Value Free: 0.259
- R-Value Work: 0.225
- R-Value Observed: 0.226
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 |
| GTP-binding nuclear protein Ran | 216 | Homo sapiens | Mutation(s): 1 Gene Names: RAN, ARA24, OK/SW-cl.81 |  | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P62826 (Homo sapiens) Explore P62826 Go to UniProtKB: P62826 | |||||
PHAROS: P62826 GTEx: ENSG00000132341 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P62826 | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Ran-specific GTPase-activating protein 1 | 140 | Saccharomyces cerevisiae S288C | Mutation(s): 0 Gene Names: YRB1, CST20, HTN1, SFO1, YDR002W, YD8119.08 |  | |
UniProt | |||||
Find proteins for P41920 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P41920 Go to UniProtKB: P41920 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P41920 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 3 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Exportin-1,Exportin-1 | 1,024 | Saccharomyces cerevisiae S288C | Mutation(s): 5 Gene Names: CRM1, KAP124, XPO1, YGR218W, G8514 |  | |
UniProt | |||||
Find proteins for P30822 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P30822 Go to UniProtKB: P30822 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P30822 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 4 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| GTP Query on GTP | D [auth A] | GUANOSINE-5'-TRIPHOSPHATE C10 H16 N5 O14 P3 XKMLYUALXHKNFT-UUOKFMHZSA-N |  | ||
| D29 (Subject of Investigation/LOI) Query on D29 | F [auth C] | (Z)-{[(3E)-4-{(R)-[3,5-bis(trifluoromethyl)phenyl]sulfinyl}but-3-en-1-yl]imino}methanethiol C13 H11 F6 N O S2 LCTALRIGMZILGK-KFVKGYIZSA-N |  | ||
| CL Query on CL | G [auth C] | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M |  | ||
| MG Query on MG | E [auth A] | MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.60 Å
- R-Value Free: 0.259
- R-Value Work: 0.225
- R-Value Observed: 0.226
- Space Group: P 43 21 2
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 105.438 | α = 90 |
| b = 105.438 | β = 90 |
| c = 303.907 | γ = 90 |
| Software Name | Purpose |
|---|---|
| HKL-2000 | data scaling |
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
| HKL-2000 | data reduction |
| MOLREP | phasing |
Entry History
Revision History (Full details and data files)
- Version 1.0: 2019-04-17
Type: Initial release - Version 1.1: 2023-11-22
Changes: Data collection, Database references, Derived calculations, Refinement description
