1GXS
Crystal Structure of Hydroxynitrile Lyase from Sorghum bicolor in Complex with Inhibitor Benzoic Acid: a novel cyanogenic enzyme
- PDB DOI: https://doi.org/10.2210/pdb1GXS/pdb
- Classification: LYASE
- Organism(s): Sorghum bicolor
- Mutation(s): Yes 
- Deposited: 2002-04-11 Released: 2002-10-01 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.30 Å
- R-Value Free: 0.222 
- R-Value Work: 0.165 
- R-Value Observed: 0.165 
This is version 2.1 of the entry. See complete history. 
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
P-(S)-HYDROXYMANDELONITRILE LYASE CHAIN A | 270 | Sorghum bicolor | Mutation(s): 4  EC: 4.1.2.11 | ||
UniProt | |||||
Find proteins for P52708 (Sorghum bicolor) Explore P52708  Go to UniProtKB:  P52708 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P52708 | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
P-(S)-HYDROXYMANDELONITRILE LYASE CHAIN B | 158 | Sorghum bicolor | Mutation(s): 3  EC: 4.1.2.11 | ||
UniProt | |||||
Find proteins for P52708 (Sorghum bicolor) Explore P52708  Go to UniProtKB:  P52708 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P52708 | ||||
Sequence AnnotationsExpand | |||||
|
Oligosaccharides
Small Molecules
Ligands 3 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
NAG Query on NAG | I [auth B], L [auth D] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N | |||
DKA Query on DKA | H [auth A], K [auth C] | DECANOIC ACID C10 H20 O2 GHVNFZFCNZKVNT-UHFFFAOYSA-N | |||
BEZ Query on BEZ | G [auth A], J [auth C] | BENZOIC ACID C7 H6 O2 WPYMKLBDIGXBTP-UHFFFAOYSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.30 Å
- R-Value Free: 0.222 
- R-Value Work: 0.165 
- R-Value Observed: 0.165 
- Space Group: C 1 2 1
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 150.7 | α = 90 |
b = 103.7 | β = 101.3 |
c = 90.6 | γ = 90 |
Software Name | Purpose |
---|---|
X-PLOR | refinement |
MOSFLM | data reduction |
SCALEPACK | data scaling |
X-PLOR | phasing |
Entry History 
Deposition Data
- Released Date: 2002-10-01  Deposition Author(s): Lauble, H., Miehlich, B., Foerster, S., Wajant, H., Effenberger, F.
Revision History (Full details and data files)
- Version 1.0: 2002-10-01
Type: Initial release - Version 1.1: 2011-10-26
Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Other, Structure summary, Version format compliance - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Other, Structure summary - Version 2.1: 2023-12-13
Changes: Data collection, Database references, Refinement description, Structure summary