Download MendeleyCrystal structure of spermidine synthase from Pyrococcus horikoshii OT3
Mizutani, H., Kunishima, N.To be published.
2E5W
Crystal structure of spermidine synthase from Pyrococcus horikoshii OT3
- PDB DOI: https://doi.org/10.2210/pdb2E5W/pdb
- Classification: TRANSFERASE
- Organism(s): Pyrococcus horikoshii OT3
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2006-12-25 Released: 2007-06-26
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.00 Å
- R-Value Free: 0.215
- R-Value Work: 0.194
- R-Value Observed: 0.194
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 |
| Probable spermidine synthase | 280 | Pyrococcus horikoshii OT3 | Mutation(s): 0 EC: 2.5.1.16 |  | |
UniProt | |||||
Find proteins for O57950 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)) Explore O57950 Go to UniProtKB: O57950 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | O57950 | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| MTA Query on MTA | G [auth A], K [auth C] | 5'-DEOXY-5'-METHYLTHIOADENOSINE C11 H15 N5 O3 S WUUGFSXJNOTRMR-IOSLPCCCSA-N |  | ||
| AG3 Query on AG3 | F [auth A], J [auth C] | 1-{4-[(3-aminopropyl)amino]butyl}guanidine C8 H21 N5 XYCUJKFFVBCJEF-UHFFFAOYSA-N |  | ||
| ACT Query on ACT | E [auth A], H [auth B], I [auth C], L [auth D] | ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.00 Å
- R-Value Free: 0.215
- R-Value Work: 0.194
- R-Value Observed: 0.194
- Space Group: C 1 2 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 149.411 | α = 90 |
| b = 122.735 | β = 117.69 |
| c = 102.085 | γ = 90 |
| Software Name | Purpose |
|---|---|
| CNS | refinement |
| HKL-2000 | data collection |
| HKL-2000 | data reduction |
| HKL-2000 | data scaling |
| MOLREP | phasing |
Entry History
Deposition Data
- Released Date: 2007-06-26 Deposition Author(s): Mizutani, H., Kunishima, N., RIKEN Structural Genomics/Proteomics Initiative (RSGI)
Revision History (Full details and data files)
- Version 1.0: 2007-06-26
Type: Initial release - Version 1.1: 2008-04-30
Changes: Version format compliance - Version 1.2: 2011-07-13
Changes: Source and taxonomy, Version format compliance - Version 1.3: 2023-10-25
Changes: Data collection, Database references, Derived calculations, Refinement description
