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.
1VC8
Crystal Structure of a T.thermophilus HB8 Ap6A Hydrolase Ndx1-Ap6A Complex
- PDB DOI: https://doi.org/10.2210/pdb1VC8/pdb
- Classification: HYDROLASE
- Organism(s): Thermus thermophilus HB8
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No
- Deposited: 2004-03-05 Released: 2005-04-26
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.00 Å
- R-Value Free: 0.225
- R-Value Work: 0.195
- R-Value Observed: 0.195
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 |
| Ndx1 | 126 | Thermus thermophilus HB8 | Mutation(s): 0 Gene Names: ndx1 EC: 3.6.1.61 |  | |
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 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| 5FA Query on 5FA | C [auth A], D [auth B] | ADENOSINE-5'-PENTAPHOSPHATE C10 H18 N5 O19 P5 WYJWVZZCMBUPSP-KQYNXXCUSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.00 Å
- R-Value Free: 0.225
- R-Value Work: 0.195
- R-Value Observed: 0.195
- Space Group: P 21 21 21
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 52.413 | α = 90 |
| b = 54.775 | β = 90 |
| c = 111.673 | 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: 2023-12-27
Changes: Data collection, Database references, Derived calculations
