2X3T
Glutaraldehyde-crosslinked wheat germ agglutinin isolectin 1 crystal soaked with a synthetic glycopeptide
- PDB DOI: https://doi.org/10.2210/pdb2X3T/pdb
- Classification: SUGAR BINDING PROTEIN/PEPTIDE
- Organism(s): Triticum aestivum, synthetic construct
- Mutation(s): No 
- Deposited: 2010-01-26 Released: 2010-06-30 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.75 Å
- R-Value Free: 0.285 
- R-Value Work: 0.229 
- R-Value Observed: 0.232 
This is version 4.1 of the entry. See complete history. 
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
AGGLUTININ ISOLECTIN 1 | 171 | Triticum aestivum | Mutation(s): 0  | ||
UniProt | |||||
Find proteins for P10968 (Triticum aestivum) Explore P10968  Go to UniProtKB:  P10968 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P10968 | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by: Sequence | 3D Structure
Entity ID: 2 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
GLYCOPEPTIDE | E, F [auth M] | 9 | synthetic construct | Mutation(s): 0  | |
Sequence AnnotationsExpand | |||||
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Small Molecules
Ligands 3 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
GYV Query on GYV | AA [auth M] G [auth A] I [auth A] L [auth B] N [auth B] | 2-acetamido-1-O-carbamoyl-2-deoxy-alpha-D-glucopyranose C9 H16 N2 O7 BMFDLZBABRHLIB-FMDGEEDCSA-N | |||
DBB Query on DBB | H [auth A] J [auth A] M [auth B] O [auth B] R [auth C] | D-ALPHA-AMINOBUTYRIC ACID C4 H9 N O2 QWCKQJZIFLGMSD-GSVOUGTGSA-N | |||
GOL Query on GOL | K [auth A], P [auth B], W [auth D] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |
Modified Residues 1 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Type | Formula | 2D Diagram | Parent |
PCA Query on PCA | A, B, C, D | L-PEPTIDE LINKING | C5 H7 N O3 | GLN |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.75 Å
- R-Value Free: 0.285 
- R-Value Work: 0.229 
- R-Value Observed: 0.232 
- Space Group: P 1 21 1
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 44.64 | α = 90 |
b = 93.21 | β = 98.32 |
c = 92.5 | γ = 90 |
Software Name | Purpose |
---|---|
PHENIX | refinement |
XDS | data reduction |
XSCALE | data scaling |
MOLREP | phasing |
Entry History 
Deposition Data
- Released Date: 2010-06-30  Deposition Author(s): Schwefel, D., Maierhofer, C., Wittmann, V., Diederichs, K., Welte, W.
Revision History (Full details and data files)
- Version 1.0: 2010-06-30
Type: Initial release - Version 1.1: 2014-04-09
Changes: Derived calculations, Non-polymer description, Refinement description, Version format compliance - Version 1.2: 2016-12-28
Changes: Source and taxonomy - Version 2.0: 2020-03-11
Changes: Derived calculations, Other, Polymer sequence - Version 3.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary - Version 4.0: 2020-08-05
Changes: Atomic model, Derived calculations, Structure summary - Version 4.1: 2023-12-20
Changes: Data collection, Database references, Derived calculations, Refinement description