5ELE

Cholera toxin El Tor B-pentamer in complex with A Lewis-y

PDB DOI: https://doi.org/10.2210/pdb5ELE/pdb

Classification: TOXIN
Organism(s): Vibrio cholerae O1
Expression System: Vibrio sp.
Mutation(s): No

Deposited: 2015-11-04 Released: 2016-03-30
Deposition Author(s): Heggelund, J.E., Burschowsky, D., Krengel, U.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.226
R-Value Work: 0.183
R-Value Observed: 0.185

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 122.39 kDa
Atom Count: 9,722
Modelled Residue Count: 1,030
Deposited Residue Count: 1,030
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cholera enterotoxin subunit B	A, B, C, D, E A, B, C, D, E, F, G, H, I, J	103	Vibrio cholerae O1	Mutation(s): 0 Gene Names: ctxB, toxB, VC_1456
UniProt
Find proteins for P01556 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)) Explore P01556 Go to UniProtKB: P01556
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P01556
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-L-fucopyranose-(1-2)-[2-acetamido-2-deoxy-alpha-D-galactopyranose-(1-3)]beta-D-galactopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-alpha-D-glucopyranose	K, L, M	5		N/A	Interactions Focus chain K Focus chain L Focus chain M Interactions & Density Focus chain K Focus chain L Focus chain M
Glycosylation Resources
GlyTouCan: G62623TF GlyCosmos: G62623TF GlyGen: G62623TF

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
1PE Query on 1PE Download Ideal Coordinates CCD File SDF format, chain JA [auth F] MOL2 format, chain JA [auth F]	JA [auth F]	PENTAETHYLENE GLYCOL C₁₀ H₂₂ O₆ JLFNLZLINWHATN-UHFFFAOYSA-N		Interactions Focus chain JA [auth F] Interactions & Density Focus chain JA [auth F]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain KA [auth G] MOL2 format, chain KA [auth G]	KA [auth G]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain KA [auth G] Interactions & Density Focus chain KA [auth G]
FUC Query on FUC Download Ideal Coordinates CCD File SDF format, chain IA [auth F] SDF format, chain LA [auth H] SDF format, chain MA [auth I] SDF format, chain O [auth A] MOL2 format, chain IA [auth F] MOL2 format, chain LA [auth H] MOL2 format, chain MA [auth I] MOL2 format, chain O [auth A]	IA [auth F], LA [auth H], MA [auth I], O [auth A]	alpha-L-fucopyranose C₆ H₁₂ O₅ SHZGCJCMOBCMKK-SXUWKVJYSA-N		Interactions Focus chain IA [auth F] Focus chain LA [auth H] Focus chain MA [auth I] Focus chain O [auth A] Interactions & Density Focus chain IA [auth F] Focus chain LA [auth H] Focus chain MA [auth I] Focus chain O [auth A]
BCN Query on BCN Download Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain CA [auth D] SDF format, chain EA [auth E] SDF format, chain GA [auth E] SDF format, chain P [auth A] SDF format, chain R [auth A] SDF format, chain S [auth B] SDF format, chain U [auth B] SDF format, chain W [auth C] SDF format, chain Y [auth C] MOL2 format, chain AA [auth D] MOL2 format, chain CA [auth D] MOL2 format, chain EA [auth E] MOL2 format, chain GA [auth E] MOL2 format, chain P [auth A] MOL2 format, chain R [auth A] MOL2 format, chain S [auth B] MOL2 format, chain U [auth B] MOL2 format, chain W [auth C] MOL2 format, chain Y [auth C]	AA [auth D] CA [auth D] EA [auth E] GA [auth E] P [auth A] AA [auth D], CA [auth D], EA [auth E], GA [auth E], P [auth A], R [auth A], S [auth B], U [auth B], W [auth C], Y [auth C]	BICINE C₆ H₁₃ N O₄ FSVCELGFZIQNCK-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain CA [auth D] Focus chain EA [auth E] Focus chain GA [auth E] Focus chain P [auth A] Focus chain R [auth A] Focus chain S [auth B] Focus chain U [auth B] Focus chain W [auth C] Focus chain Y [auth C] Interactions & Density Focus chain AA [auth D] Focus chain CA [auth D] Focus chain EA [auth E] Focus chain GA [auth E] Focus chain P [auth A] Focus chain R [auth A] Focus chain S [auth B] Focus chain U [auth B] Focus chain W [auth C] Focus chain Y [auth C]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain X [auth C] SDF format, chain BA [auth D] SDF format, chain DA [auth D] SDF format, chain FA [auth E] SDF format, chain HA [auth E] SDF format, chain N [auth A] SDF format, chain Q [auth A] SDF format, chain T [auth B] SDF format, chain V [auth B] SDF format, chain Z [auth C] MOL2 format, chain X [auth C] MOL2 format, chain BA [auth D] MOL2 format, chain DA [auth D] MOL2 format, chain FA [auth E] MOL2 format, chain HA [auth E] MOL2 format, chain N [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain T [auth B] MOL2 format, chain V [auth B] MOL2 format, chain Z [auth C]	BA [auth D] DA [auth D] FA [auth E] HA [auth E] N [auth A] BA [auth D], DA [auth D], FA [auth E], HA [auth E], N [auth A], Q [auth A], T [auth B], V [auth B], X [auth C], Z [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain BA [auth D] Focus chain DA [auth D] Focus chain FA [auth E] Focus chain HA [auth E] Focus chain N [auth A] Focus chain Q [auth A] Focus chain T [auth B] Focus chain V [auth B] Focus chain X [auth C] Focus chain Z [auth C] Interactions & Density Focus chain BA [auth D] Focus chain DA [auth D] Focus chain FA [auth E] Focus chain HA [auth E] Focus chain N [auth A] Focus chain Q [auth A] Focus chain T [auth B] Focus chain V [auth B] Focus chain X [auth C] Focus chain Z [auth C]

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900128 Query on PRD_900128	K, L, M	Blood group A Lewis Y antigen, alpha anomer	Oligosaccharide / Antigen		Interactions Focus chain K Focus chain L Focus chain M Interactions & Density Focus chain K Focus chain L Focus chain M

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.226
R-Value Work: 0.183
R-Value Observed: 0.185
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.543	α = 90
b = 82.973	β = 90
c = 196.555	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
MOLREP	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

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 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2024-01-10
Changes: Data collection, Database references, Refinement description, Structure summary