3LEK
Lectin Domain of Lectinolysin complexed with Lewis B Antigen
- PDB DOI: https://doi.org/10.2210/pdb3LEK/pdb
- Classification: BLOOD CLOTTING
- Organism(s): Streptococcus mitis
- Expression System: Escherichia coli
- Mutation(s): Yes 
- Deposited: 2010-01-15 Released: 2010-12-29 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.00 Å
- R-Value Free: 0.237 
- R-Value Work: 0.202 
- R-Value Observed: 0.204 
wwPDB Validation   3D Report Full Report
This is version 2.2 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 |
Platelet aggregation factor Sm-hPAF | 153 | Streptococcus mitis | Mutation(s): 1  Gene Names: samhpaf | ||
UniProt | |||||
Find proteins for Q2PHL4 (Streptococcus mitis) Explore Q2PHL4  Go to UniProtKB:  Q2PHL4 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | Q2PHL4 | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
Small Molecules
Ligands 2 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
NI Query on NI | D [auth A] | NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N | |||
CA Query on CA | C [auth A] | CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N |
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2 | |||||
---|---|---|---|---|---|
ID | Chains | Name | Type/Class | 2D Diagram | 3D Interactions |
PRD_900085 Query on PRD_900085 | B | Lewis B antigen, alpha anomer | Oligosaccharide / Antigen |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.00 Å
- R-Value Free: 0.237 
- R-Value Work: 0.202 
- R-Value Observed: 0.204 
- Space Group: P 43 21 2
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 67.01 | α = 90 |
b = 67.01 | β = 90 |
c = 97.65 | γ = 90 |
Software Name | Purpose |
---|---|
d*TREK | data scaling |
PHASER | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
CrystalClear | data collection |
d*TREK | data reduction |
Entry History 
Deposition Data
- Released Date: 2010-12-29  Deposition Author(s): Feil, S.C.
Revision History (Full details and data files)
- Version 1.0: 2010-12-29
Type: Initial release - Version 1.1: 2011-07-13
Changes: Version format compliance - Version 1.2: 2012-02-29
Changes: Database references - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary - Version 2.1: 2021-10-13
Changes: Database references, Structure summary - Version 2.2: 2023-09-06
Changes: Data collection, Refinement description