Download MendeleyCrystal Structure of Nudix Protein Ndx1 from Thermus thermophilus HB8 in binary complex with diadenosine hexaphosphate
Iwai, T., Nakagawa, N., Kuramitsu, S., Masui, R.To be published.
1VC9
Crystal Structure of a T.thermophilus HB8 Ap6A hydrolase E50Q mutant-Mg2+-ATP complex
- PDB DOI: https://doi.org/10.2210/pdb1VC9/pdb
- Classification: HYDROLASE
- Organism(s): Thermus thermophilus HB8
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): Yes
- Deposited: 2004-03-05 Released: 2005-04-26
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.30 Å
- R-Value Free: 0.252
- R-Value Work: 0.216
- R-Value Observed: 0.216
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 |
| Ndx1 | 126 | Thermus thermophilus HB8 | Mutation(s): 1 Gene Names: ndx1 |  | |
UniProt | |||||
Find proteins for Q75UV1 (Thermus thermophilus) Explore Q75UV1 Go to UniProtKB: Q75UV1 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q75UV1 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| ATP Query on ATP | D [auth A], E [auth B] | ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N |  | ||
| MG Query on MG | C [auth A] | MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.30 Å
- R-Value Free: 0.252
- R-Value Work: 0.216
- R-Value Observed: 0.216
- Space Group: P 21 21 21
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 47.9 | α = 90 |
| b = 55.121 | β = 90 |
| c = 113.869 | γ = 90 |
| Software Name | Purpose |
|---|---|
| CNS | refinement |
| DENZO | data reduction |
| SCALEPACK | data scaling |
| MLPHARE | phasing |
Entry History
Deposition Data
- Released Date: 2005-04-26 Deposition Author(s): Iwai, T., Nakagawa, N., Kuramitsu, S., Masui, R., RIKEN Structural Genomics/Proteomics Initiative (RSGI)
Revision History (Full details and data files)
- Version 1.0: 2005-04-26
Type: Initial release - Version 1.1: 2008-04-27
Changes: Version format compliance - Version 1.2: 2011-07-13
Changes: Source and taxonomy, Version format compliance - Version 1.3: 2021-11-10
Changes: Database references, Derived calculations - Version 1.4: 2023-12-27
Changes: Data collection
