Download MendeleyCrystal structure of plexin A2 RBD in complex with Rnd1
Wang, H., Tempel, W., Tong, Y., Guan, X., Shen, L., Buren, L., Zhang, N., Wernimont, A.K., Crombet, L., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Weigelt, J., Park, H.To be published.
3Q3J
Crystal structure of plexin A2 RBD in complex with Rnd1
- PDB DOI: https://doi.org/10.2210/pdb3Q3J/pdb
- Classification: Membrane protein/protein binding
- Organism(s): Homo sapiens
- Expression System: Escherichia coli BL21
- Mutation(s): No
- Deposited: 2010-12-21 Released: 2011-01-12
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.97 Å
- R-Value Free: 0.248 (Depositor), 0.240 (DCC)
- R-Value Work: 0.211 (Depositor), 0.210 (DCC)
- R-Value Observed: 0.213 (Depositor)
Starting Models: experimental
View more details
This is version 1.3 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 |
| Plexin-A2 | 112 | Homo sapiens | Mutation(s): 0 Gene Names: PLXNA2, KIAA0463, OCT, PLXN2, UNQ209/PRO235 |  | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for O75051 (Homo sapiens) Explore O75051 Go to UniProtKB: O75051 | |||||
PHAROS: O75051 GTEx: ENSG00000076356 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | O75051 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Rho-related GTP-binding protein Rho6 | 214 | Homo sapiens | Mutation(s): 0 Gene Names: RND1, RHO6 |  | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for Q92730 (Homo sapiens) Explore Q92730 Go to UniProtKB: Q92730 | |||||
PHAROS: Q92730 GTEx: ENSG00000172602 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q92730 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| GNP Query on GNP | E [auth B] | PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER C10 H17 N6 O13 P3 UQABYHGXWYXDTK-UUOKFMHZSA-N |  | ||
| MG Query on MG | F [auth B] | MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N |  | ||
| UNX Query on UNX | C [auth A] D [auth A] G [auth B] H [auth B] I [auth B] | UNKNOWN ATOM OR ION X |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.97 Å
- R-Value Free: 0.248 (Depositor), 0.240 (DCC)
- R-Value Work: 0.211 (Depositor), 0.210 (DCC)
- R-Value Observed: 0.213 (Depositor)
Space Group: I 2 2 2
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 59.022 | α = 90 |
| b = 67.129 | β = 90 |
| c = 145.291 | γ = 90 |
| Software Name | Purpose |
|---|---|
| DENZO | data reduction |
| SCALEPACK | data scaling |
| MOLREP | phasing |
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
| SBC-Collect | data collection |
| HKL-3000 | data reduction |
| HKL-3000 | data scaling |
Entry History
Deposition Data
- Released Date: 2011-01-12 Deposition Author(s): Wang, H., Tempel, W., Tong, Y., Guan, X., Shen, L., Buren, L., Zhang, N., Wernimont, A.K., Crombet, L., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Weigelt, J., Park, H., Structural Genomics Consortium (SGC)
Revision History (Full details and data files)
- Version 1.0: 2011-01-12
Type: Initial release - Version 1.1: 2011-07-13
Changes: Version format compliance - Version 1.2: 2017-11-08
Changes: Refinement description - Version 1.3: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description
