Download MendeleyReshaping Substrate-Binding Pocket of Leucine Dehydrogenase for Bidirectionally Accessing Structurally Diverse Substrates
Wu, T., Wang, Y., Zhang, N., Yin, D., Xu, Y., Nie, Y., Mu, X.(2023) ACS Catal 13: 158-168
8GXD
L-LEUCINE DEHYDROGENASE FROM EXIGUOBACTERIUM SIBIRICUM
- PDB DOI: https://doi.org/10.2210/pdb8GXD/pdb
- Classification: OXIDOREDUCTASE
- Organism(s): Exiguobacterium sibiricum 255-15
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2022-09-19 Released: 2023-04-26
- Funding Organization(s): National Natural Science Foundation of China (NSFC)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 3.02 Å
- R-Value Free: 0.255
- R-Value Work: 0.213
- R-Value Observed: 0.216
wwPDB Validation 3D Report Full Report
This is version 1.1 of the entry. See complete history.
Literature
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Glu/Leu/Phe/Val dehydrogenase | 374 | Exiguobacterium sibiricum 255-15 | Mutation(s): 0 Gene Names: Exig_0916 EC: 1.4.1.9 |  | |
UniProt | |||||
Find proteins for B1YLR3 (Exiguobacterium sibiricum (strain DSM 17290 / CIP 109462 / JCM 13490 / 255-15)) Explore B1YLR3 Go to UniProtKB: B1YLR3 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | B1YLR3 | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| GOL (Subject of Investigation/LOI) Query on GOL | B [auth A], C [auth A], D [auth A] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | ||
| CA (Subject of Investigation/LOI) Query on CA | E [auth A], F [auth A], G [auth A], H [auth A] | CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 3.02 Å
- R-Value Free: 0.255
- R-Value Work: 0.213
- R-Value Observed: 0.216
- Space Group: I 4 2 2
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 152.99 | α = 90 |
| b = 152.99 | β = 90 |
| c = 132.02 | γ = 90 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
| XDS | data reduction |
| Aimless | data scaling |
| REFMAC | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2023-04-26 Deposition Author(s): Mu, X., Nie, Y., Wu, T., Wang, Y., Zhang, N., Yin, D., Xu, Y.
| Funding Organization | Location | Grant Number |
|---|---|---|
| National Natural Science Foundation of China (NSFC) | China | 21336009 |
| National Natural Science Foundation of China (NSFC) | China | 21176103 |
Revision History (Full details and data files)
- Version 1.0: 2023-04-26
Type: Initial release - Version 1.1: 2023-11-08
Changes: Data collection, Refinement description
