Download MendeleyCrystal structure of 5'-nucleotidase precursor from Thermus thermophilus HB8
Nakakaga, N., Kishishita, S., Yokoyama, S., Kuramitsu, S.To be published.
2Z1A
Crystal structure of 5'-nucleotidase precursor from Thermus thermophilus HB8
- PDB DOI: https://doi.org/10.2210/pdb2Z1A/pdb
- Classification: HYDROLASE
- Organism(s): Thermus thermophilus HB8
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2007-05-08 Released: 2007-11-13
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.75 Å
- R-Value Free: 0.209
- R-Value Work: 0.179
- R-Value Observed: 0.179
This is version 1.2 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 |
| 5'-nucleotidase | 552 | Thermus thermophilus HB8 | Mutation(s): 0 EC: 3.1.3.5 |  | |
UniProt | |||||
Find proteins for Q5SIP1 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SIP1 Go to UniProtKB: Q5SIP1 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q5SIP1 | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| THM Query on THM | E [auth A] | THYMIDINE C10 H14 N2 O5 IQFYYKKMVGJFEH-XLPZGREQSA-N |  | ||
| PO4 Query on PO4 | B [auth A] | PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K |  | ||
| ZN Query on ZN | C [auth A], D [auth A] | ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.75 Å
- R-Value Free: 0.209
- R-Value Work: 0.179
- R-Value Observed: 0.179
- Space Group: P 1 21 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 55.426 | α = 90 |
| b = 57.832 | β = 105.95 |
| c = 81.96 | γ = 90 |
| Software Name | Purpose |
|---|---|
| CNS | refinement |
| HKL-2000 | data reduction |
| HKL-2000 | data scaling |
| MOLREP | phasing |
Entry History
Deposition Data
- Released Date: 2007-11-13 Deposition Author(s): Nakagawa, N., Kishishita, S., Yokoyama, S., Kuramitsu, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)
Revision History (Full details and data files)
- Version 1.0: 2007-11-13
Type: Initial release - Version 1.1: 2011-07-13
Changes: Source and taxonomy, Version format compliance - Version 1.2: 2023-11-01
Changes: Data collection, Database references, Derived calculations, Refinement description
