Download MendeleyCrystal structure of human RAB3D in complex with GDP
Hong, B., Wang, J., Shen, L., Tempel, W., Landry, R., Arrowsmith, C.H., Edwards, A.M., Sundstrom, M., Weigelt, J., Bochkarev, A., Park, H.To be published.
2GF9
Crystal structure of human RAB3D in complex with GDP
- PDB DOI: https://doi.org/10.2210/pdb2GF9/pdb
- Classification: PROTEIN TRANSPORT
- Organism(s): Homo sapiens
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2006-03-21 Released: 2006-05-02
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.53 Å
- R-Value Free: 0.185
- R-Value Work: 0.153
This is version 1.3 of the entry. See complete history.
Literature
To be published.
Macromolecules
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(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Ras-related protein Rab-3D | A | 189 | Homo sapiens | Mutation(s): 0 Gene Names: RAB3D, GOV, RAB16 |  |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for O95716 (Homo sapiens) Explore O95716 Go to UniProtKB: O95716 | |||||
PHAROS: O95716 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | O95716 | ||||
Protein Feature ViewExpand | |||||
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Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| GDP Query on GDP | E [auth A] | GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N |  | Ligand Interaction | |
| MG Query on MG | B [auth A] | MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N |  | Ligand Interaction | |
| UNX Query on UNX | C [auth A], D [auth A] | UNKNOWN ATOM OR ION X |  | Ligand Interaction | |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.53 Å
- R-Value Free: 0.185
- R-Value Work: 0.153
- Space Group: P 21 21 21
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 35.7 | α = 90 |
| b = 63.222 | β = 90 |
| c = 67.695 | γ = 90 |
| Software Name | Purpose |
|---|---|
| DENZO | data reduction |
| SCALEPACK | data scaling |
| PHASER | phasing |
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
Entry History
Deposition Data
- Released Date: 2006-05-02 Deposition Author(s): Hong, B., Wang, J., Shen, L., Tempel, W., Landry, R., Arrowsmith, C.H., Edwards, A.M., Sundstrom, M., Weigelt, J., Bochkarev, A., Park, H., Structural Genomics Consortium (SGC)
Revision History (Full details and data files)
- Version 1.0: 2006-05-02
Type: Initial release - Version 1.1: 2008-05-01
Changes: Version format compliance - Version 1.2: 2011-07-13
Changes: Version format compliance - Version 1.3: 2017-10-18
Changes: Refinement description
