Download MendeleyCrystal structure of human RAB5B in complex with GDP
Hong, B., Shen, L., Wang, J., Tempel, W., Landry, R., Arrowsmith, C.H., Edwards, A.M., Sundstrom, M., Weigelt, J., Bochkarev, A., Park, H.To be published.
2HEI
Crystal structure of human RAB5B in complex with GDP
- PDB DOI: https://doi.org/10.2210/pdb2HEI/pdb
- Classification: TRANSPORT PROTEIN
- Organism(s): Homo sapiens
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2006-06-21 Released: 2006-07-04
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.55 ?
- R-Value Free: 0.294
- R-Value Work: 0.262
Starting Model: experimental
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This is version 1.4 of the entry. See complete history.
Literature
To be published.
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Ras-related protein Rab-5B | 179 | Homo sapiens | Mutation(s): 0 Gene Names: RAB5B EC: 3.6.5.2 |  | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P61020 (Homo sapiens) Explore P61020 Go to UniProtKB: P61020 | |||||
PHAROS: P61020 GTEx: ENSG00000111540 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P61020 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| GDP Query on GDP | C [auth A], E [auth B] | GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N |  | ||
| D1D Query on D1D | D [auth A], F [auth B] | (4S,5S)-1,2-DITHIANE-4,5-DIOL C4 H8 O2 S2 YPGMOWHXEQDBBV-QWWZWVQMSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.55 ?
- R-Value Free: 0.294
- R-Value Work: 0.262
- Space Group: P 21 21 21
Unit Cell:
| Length ( ? ) | Angle ( ? ) |
|---|---|
| a = 41.302 | ¦Á = 90 |
| b = 78.37 | ¦Â = 90 |
| c = 95.501 | ¦Ă = 90 |
| Software Name | Purpose |
|---|---|
| DENZO | data reduction |
| SCALEPACK | data scaling |
| PHASER | phasing |
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
| ARP/wARP | model building |
| MolProbity | model building |
Entry History
Deposition Data
- Released Date: 2006-07-04 Deposition Author(s): Hong, B., Shen, L., Wang, J., 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: 2006-07-04
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 - Version 1.4: 2023-08-30
Changes: Data collection, Database references, Derived calculations, Refinement description
