5ELB
Cholera toxin classical B-pentamer in complex with Lewis-y
- PDB DOI: https://doi.org/10.2210/pdb5ELB/pdb
- Classification: TOXIN
- Organism(s): Vibrio cholerae O1
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No 
- Deposited: 2015-11-04 Released: 2016-03-30 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.08 Å
- R-Value Free: 0.155 
- R-Value Work: 0.120 
- R-Value Observed: 0.122 
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 |
Cholera enterotoxin B subunit | 103 | Vibrio cholerae O1 | Mutation(s): 0  Gene Names: ctxB, EN12_07055, ERS013160_03498, ERS013165_03981, ERS013197_06217, ERS013202_03762, ERS013206_03003, ERS013207_03244, ERS013212_03447 | ||
UniProt | |||||
Find proteins for Q57193 (Vibrio cholerae) Explore Q57193  Go to UniProtKB:  Q57193 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | Q57193 | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
Entity ID: 2 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-alpha-D-glucopyranose | K, L, M, N, O K, L, M, N, O, P, Q, R | 4 | N/A | ||
Glycosylation Resources | |||||
GlyTouCan:  G82236PZ GlyCosmos:  G82236PZ GlyGen:  G82236PZ |
Entity ID: 3 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-3)-alpha-L-fucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose | S, T | 5 | N/A | N/A |
Small Molecules
Ligands 5 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
GLA Query on GLA | BB [auth G] DA [auth B] EB [auth H] GB [auth I] IA [auth C] | alpha-D-galactopyranose C6 H12 O6 WQZGKKKJIJFFOK-PHYPRBDBSA-N | |||
GAL Query on GAL | CA [auth B] CB [auth G] DB [auth H] FB [auth I] HA [auth C] | beta-D-galactopyranose C6 H12 O6 WQZGKKKJIJFFOK-FPRJBGLDSA-N | |||
BCN Query on BCN | BA [auth B] FA [auth B] KA [auth C] LA [auth C] MA [auth D] | BICINE C6 H13 N O4 FSVCELGFZIQNCK-UHFFFAOYSA-N | |||
PEG Query on PEG | AB [auth G] | DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N | |||
CA Query on CA | AA [auth B] EA [auth B] GA [auth C] JA [auth C] NA [auth D] | 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_900124 Query on PRD_900124 | K, L, M, N, O | Lewis Y antigen, alpha anomer | Oligosaccharide / Antigen |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.08 Å
- R-Value Free: 0.155 
- R-Value Work: 0.120 
- R-Value Observed: 0.122 
- Space Group: P 21 21 21
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 72.333 | α = 90 |
b = 98.984 | β = 90 |
c = 152.019 | γ = 90 |
Software Name | Purpose |
---|---|
REFMAC | refinement |
XDS | data reduction |
XDS | data scaling |
PHASER | phasing |
Entry History 
Deposition Data
- Released Date: 2016-03-30  Deposition Author(s): Heggelund, J.E., Burschowsky, D., Krengel, U.
Revision History (Full details and data files)
- Version 1.0: 2016-03-30
Type: Initial release - Version 1.1: 2016-04-27
Changes: Database references - Version 1.2: 2017-10-11
Changes: Derived calculations - Version 1.3: 2018-11-21
Changes: Data collection, Source and taxonomy - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary - Version 2.1: 2024-01-10
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary