2HOR
Crystal structure of alliinase from garlic- apo form
- PDB DOI: https://doi.org/10.2210/pdb2HOR/pdb
- Classification: LYASE
- Organism(s): Allium sativum
- Mutation(s): No
- Deposited: 2006-07-16 Released: 2007-02-06
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.60 Å
- R-Value Free: 0.179
- R-Value Work: 0.163
- R-Value Observed: 0.164
wwPDB Validation 3D Report Full Report
This is version 2.0 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 |
| Alliin lyase 1 | 427 | Allium sativum | Mutation(s): 0 EC: 4.4.1.4 |  | |
UniProt | |||||
Find proteins for Q01594 (Allium sativum) Explore Q01594 Go to UniProtKB: Q01594 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q01594 | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
| alpha-D-mannopyranose-(2-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose | B | 6 | N/A | N-Glycosylation | |
Small Molecules
| Ligands 5 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| NAG Query on NAG | C [auth A] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N |  | ||
| SO4 Query on SO4 | D [auth A], E [auth A], G [auth A], H [auth A], I [auth A] | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L |  | ||
| NO3 Query on NO3 | L [auth A] | NITRATE ION N O3 NHNBFGGVMKEFGY-UHFFFAOYSA-N |  | ||
| ACT Query on ACT | F [auth A] | ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M |  | ||
| CL Query on CL | J [auth A], K [auth A] | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.60 Å
- R-Value Free: 0.179
- R-Value Work: 0.163
- R-Value Observed: 0.164
- Space Group: P 41 21 2
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 81.118 | α = 90 |
| b = 81.118 | β = 90 |
| c = 164.017 | γ = 90 |
| Software Name | Purpose |
|---|---|
| DENZO | data reduction |
| SCALEPACK | data scaling |
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
| HKL-2000 | data reduction |
| MOLREP | phasing |
Entry History
Deposition Data
- Released Date: 2007-02-06 Deposition Author(s): Shimon, L.J.W., Rabinkov, A., Wilcheck, M., Mirelman, D., Frolow, F.
Revision History (Full details and data files)
- Version 1.0: 2007-02-06
Type: Initial release - Version 1.1: 2008-05-01
Changes: Version format compliance - Version 1.2: 2011-07-13
Changes: Derived calculations, Version format compliance - Version 1.3: 2014-04-16
Changes: Other - Version 1.4: 2017-10-18
Changes: Advisory, Refinement description - Version 1.5: 2018-01-24
Changes: Structure summary - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
