Download MendeleyCrystal structure of apo GGTaseIII
Goto-Ito, S., Shirakawa, R., Fukai, S.To be published.
6J6X
Crystal structure of apo GGTaseIII
- PDB DOI: https://doi.org/10.2210/pdb6J6X/pdb
- Classification: LIPID BINDING PROTEIN
- Organism(s): Homo sapiens
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2019-01-16 Released: 2020-01-22
- Funding Organization(s): Japan Science and Technology, Japan Society for the Promotion of Science
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.96 Å
- R-Value Free: 0.297
- R-Value Work: 0.266
- R-Value Observed: 0.267
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 |
| Protein prenyltransferase alpha subunit repeat-containing protein 1 | 366 | Homo sapiens | Mutation(s): 0 Gene Names: PTAR1 |  | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for Q7Z6K3 (Homo sapiens) Explore Q7Z6K3 Go to UniProtKB: Q7Z6K3 | |||||
PHAROS: Q7Z6K3 GTEx: ENSG00000188647 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q7Z6K3 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Geranylgeranyl transferase type-2 subunit beta | 336 | Homo sapiens | Mutation(s): 0 Gene Names: RABGGTB, GGTB EC: 2.5.1.60 |  | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P53611 (Homo sapiens) Explore P53611 Go to UniProtKB: P53611 | |||||
PHAROS: P53611 GTEx: ENSG00000137955 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P53611 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| MPD Query on MPD | C [auth A], E [auth B] | (4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N |  | ||
| MG Query on MG | D [auth B] | MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N |  | ||
| Modified Residues 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| CAS Query on CAS | A | L-PEPTIDE LINKING | C5 H12 As N O2 S |  | CYS |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.96 Å
- R-Value Free: 0.297
- R-Value Work: 0.266
- R-Value Observed: 0.267
- Space Group: P 65 2 2
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 88.54 | α = 90 |
| b = 88.54 | β = 90 |
| c = 647.581 | γ = 120 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| HKL-2000 | data reduction |
| HKL-2000 | data scaling |
| MOLREP | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2020-01-22 Deposition Author(s): Goto-Ito, S., Yamagata, A., Sato, Y., Fukai, S.
| Funding Organization | Location | Grant Number |
|---|---|---|
| Japan Science and Technology | Japan | CREST JPMJCR12M5 |
| Japan Society for the Promotion of Science | Japan | KAKENHI 16K08574 |
| Japan Society for the Promotion of Science | Japan | KAKENHI 16H05148 |
Revision History (Full details and data files)
- Version 1.0: 2020-01-22
Type: Initial release - Version 1.1: 2023-11-22
Changes: Data collection, Database references, Refinement description
