3O5W
Binding of kinetin in the active site of mistletoe lectin I
- PDB DOI: https://doi.org/10.2210/pdb3O5W/pdb
- Classification: HYDROLASE
- Organism(s): Viscum album
- Mutation(s): No 
- Deposited: 2010-07-28 Released: 2011-09-14 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.70 Å
- R-Value Free: 0.226 
- R-Value Work: 0.174 
- R-Value Observed: 0.177 
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 |
Beta-galactoside-specific lectin 1 chain A isoform 1 | 254 | Viscum album | Mutation(s): 0  EC: 3.2.2.22 | ||
UniProt | |||||
Find proteins for P81446 (Viscum album) Explore P81446  Go to UniProtKB:  P81446 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P81446 | ||||
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 |
Beta-galactoside-specific lectin 1 chain B | 263 | Viscum album | Mutation(s): 0  EC: 3.2.2.22 | ||
UniProt | |||||
Find proteins for P81446 (Viscum album) Explore P81446  Go to UniProtKB:  P81446 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P81446 | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
Entity ID: 3 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | C, E | 2 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT |
Entity ID: 4 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | D | 3 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G47362BJ GlyCosmos:  G47362BJ GlyGen:  G47362BJ |
Small Molecules
Ligands 4 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
NAG Query on NAG | G [auth A] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N | |||
H35 Query on H35 | J [auth A] | N-(FURAN-2-YLMETHYL)-7H-PURIN-6-AMINE C10 H9 N5 O QANMHLXAZMSUEX-UHFFFAOYSA-N | |||
SO4 Query on SO4 | F [auth A] | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L | |||
GOL Query on GOL | H [auth A] I [auth A] K [auth A] L [auth A] M [auth B] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 4 | |||||
---|---|---|---|---|---|
ID | Chains | Name | Type/Class | 2D Diagram | 3D Interactions |
PRD_900017 Query on PRD_900017 | D | triacetyl-beta-chitotriose | Oligosaccharide / Inhibitor |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.70 Å
- R-Value Free: 0.226 
- R-Value Work: 0.174 
- R-Value Observed: 0.177 
- Space Group: P 65 2 2
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 107.573 | α = 90 |
b = 107.573 | β = 90 |
c = 310.633 | γ = 120 |
Software Name | Purpose |
---|---|
DENZO | data reduction |
SCALEPACK | data scaling |
PHASER | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
MAR345 | data collection |
HKL-2000 | data reduction |
Entry History 
Deposition Data
- Released Date: 2011-09-14  Deposition Author(s): Malecki, P.H., Meyer, A., Rypniewski, W., Szymanski, M., Barciszewski, J., Betzel, C.
Revision History (Full details and data files)
- Version 1.0: 2011-09-14
Type: Initial release - Version 1.1: 2012-10-10
Changes: Database references - Version 1.2: 2017-11-08
Changes: Refinement description - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Experimental preparation, Structure summary - Version 2.1: 2023-11-01
Changes: Data collection, Database references, Refinement description, Structure summary