Download MendeleyNMR fragment-based screening against the two PDZ do-mains of MDA-9
Tang, H.To be published.
8HCK
NMR fragment-based screening against the two PDZ do-mains of MDA-9
- PDB DOI: https://doi.org/10.2210/pdb8HCK/pdb
- Classification: CELL INVASION
- Organism(s): Homo sapiens
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2022-11-01 Released: 2023-11-08
- Funding Organization(s): Not funded
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.00 Å
- R-Value Free: 0.264
- R-Value Work: 0.232
- R-Value Observed: 0.237
This is version 1.0 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 |
| Syntenin-1 | 81 | Homo sapiens | Mutation(s): 0 Gene Names: SDCBP, MDA9, SYCL |  | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for O00560 (Homo sapiens) Explore O00560 Go to UniProtKB: O00560 | |||||
PHAROS: O00560 GTEx: ENSG00000137575 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | O00560 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| P1Z (Subject of Investigation/LOI) Query on P1Z | B [auth A] | 4-BUTYL-1,2-DIPHENYL-PYRAZOLIDINE-3,5-DIONE C19 H20 N2 O2 VYMDGNCVAMGZFE-UHFFFAOYSA-N |  | ||
| SO4 Query on SO4 | C [auth A], D [auth A] | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L |  | ||
| GOL Query on GOL | E [auth A], F [auth A] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.00 Å
- R-Value Free: 0.264
- R-Value Work: 0.232
- R-Value Observed: 0.237
- Space Group: P 41 2 2
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 49.353 | α = 90 |
| b = 49.353 | β = 90 |
| c = 75.254 | γ = 90 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| PDB_EXTRACT | data extraction |
| HKL-2000 | data reduction |
| HKL-2000 | data scaling |
| PHASER | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2023-11-08 Deposition Author(s): Tang, H.
| Funding Organization | Location | Grant Number |
|---|---|---|
| Not funded | -- |
Revision History (Full details and data files)
- Version 1.0: 2023-11-08
Type: Initial release
