Download MendeleyKinetic, Spectral and Structural Characterization of the Slow Binding Inhibitor Acetopyruvate with Dihydrodipicolinate Synthase from Escherichia coli.
Chooback, L., Thomas, L.M., Karsten, W.E., Fleming, C.D., Seabourn, P.To be published.
5T25
Kinetic, Spectral and Structural Characterization of the Slow Binding Inhibitor Acetopyruvate with Dihydrodipicolinate Synthase from Escherichia coli.
- PDB DOI: https://doi.org/10.2210/pdb5T25/pdb
- Classification: HYDROLASE
- Organism(s): Escherichia coli IAI1
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2016-08-23 Released: 2017-03-01
- Funding Organization(s): OK-INBRE RPI
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.99 Å
- R-Value Free: 0.211
- R-Value Work: 0.158
- R-Value Observed: 0.161
wwPDB Validation 3D Report Full Report
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 |
| 4-hydroxy-tetrahydrodipicolinate synthase | 293 | Escherichia coli IAI1 | Mutation(s): 0 Gene Names: dapA, ECIAI1_2529 EC: 4.3.3.7 |  | |
UniProt | |||||
Find proteins for B7M7I1 (Escherichia coli O8 (strain IAI1)) Explore B7M7I1 Go to UniProtKB: B7M7I1 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | B7M7I1 | ||||
Protein Feature ViewExpand | |||||
| |||||
Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| LYS Query on LYS | C [auth A], I [auth B] | LYSINE C6 H15 N2 O2 KDXKERNSBIXSRK-YFKPBYRVSA-O |  | Ligand Interaction | |
| NA Query on NA | D [auth A] E [auth A] F [auth A] G [auth A] H [auth A] | SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N |  | Ligand Interaction | |
| Modified Residues 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| 74P Query on 74P | A, B | L-PEPTIDE LINKING | C11 H18 N2 O5 |  | LYS |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.99 Å
- R-Value Free: 0.211
- R-Value Work: 0.158
- R-Value Observed: 0.161
- Space Group: C 1 2 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 136.647 | α = 90 |
| b = 56.385 | β = 127.62 |
| c = 101.53 | γ = 90 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| HKL-3000 | data reduction |
| SCALEPACK | data scaling |
| PHASER | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2017-03-01 Deposition Author(s): Chooback, L., Thomas, L.M., Karsten, W.E., Fleming, C.D., Seabourn, P.
| Funding Organization | Location | Grant Number |
|---|---|---|
| OK-INBRE RPI | United States | RS20132225112 |
Revision History (Full details and data files)
- Version 1.0: 2017-03-01
Type: Initial release - Version 1.1: 2017-05-17
Changes: Non-polymer description - Version 1.2: 2018-11-07
Changes: Data collection, Source and taxonomy - Version 1.3: 2023-10-04
Changes: Data collection, Database references, Derived calculations, Refinement description
