Download MendeleyStructure of Pea Lectin in Complex with Alpha-Methyl-D-Glucopyranoside
Shevtsov, M.B., Tsygannik, I.N.To be published.
1HKD
Structure of pea lectin in complex with alpha-methyl-D-glucopyranoside
- PDB DOI: https://doi.org/10.2210/pdb1HKD/pdb
- Classification: PLANT LECTIN
- Organism(s): Pisum sativum
- Mutation(s): No
- Deposited: 2003-03-06 Released: 2003-03-18
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.09 Å
- R-Value Free: 0.209
- R-Value Work: 0.163
- R-Value Observed: 0.165
Starting Model: experimental
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This is version 1.5 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 |
| PEA LECTIN ALPHA CHAIN | 181 | Pisum sativum | Mutation(s): 0 |  | |
UniProt | |||||
Find proteins for P02867 (Pisum sativum) Explore P02867 Go to UniProtKB: P02867 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P02867 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| PEA LECTIN BETA CHAIN | 52 | Pisum sativum | Mutation(s): 0 |  | |
UniProt | |||||
Find proteins for P02867 (Pisum sativum) Explore P02867 Go to UniProtKB: P02867 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P02867 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| GYP Query on GYP | G [auth A], J [auth C] | methyl alpha-D-glucopyranoside C7 H14 O6 HOVAGTYPODGVJG-ZFYZTMLRSA-N |  | ||
| MN Query on MN | F [auth A], I [auth C] | MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N |  | ||
| CA Query on CA | E [auth A], H [auth C] | CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.09 Å
- R-Value Free: 0.209
- R-Value Work: 0.163
- R-Value Observed: 0.165
- Space Group: P 21 21 21
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 50.793 | α = 90 |
| b = 61.235 | β = 90 |
| c = 136.005 | γ = 90 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| DENZO | data reduction |
| SCALEPACK | data scaling |
| MOLREP | phasing |
Entry History
Deposition Data
- Released Date: 2003-03-18 Deposition Author(s): Shevtsov, M.B., Tsygannik, I.N.
Revision History (Full details and data files)
- Version 1.0: 2003-03-18
Type: Initial release - Version 1.1: 2011-05-08
Changes: Version format compliance - Version 1.2: 2011-07-13
Changes: Version format compliance - Version 1.3: 2017-06-28
Changes: Data collection - Version 1.4: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Other, Structure summary - Version 1.5: 2023-12-13
Changes: Advisory, Data collection, Database references, Refinement description, Structure summary
