6HMY

Cholera toxin classical B-pentamer in complex with fucosyl-GM1

PDB DOI: https://doi.org/10.2210/pdb6HMY/pdb

Classification: TOXIN
Organism(s): Vibrio cholerae
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2018-09-13 Released: 2019-08-14
Deposition Author(s): Krengel, U., Heim, J.B.
Funding Organization(s): Research Council of Norway

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.214
R-Value Work: 0.184
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: 130.04 kDa
Atom Count: 10,879
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 B-subunit	A, B, C, D, E A, B, C, D, E, F, G, H, I, J	103	Vibrio cholerae	Mutation(s): 0 Gene Names: ctxB, C9J66_18955, EN12_07055, ERS013165_03981, ERS013197_06217, ERS013202_03762, ERS013206_03003
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)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose-(1-4)-[N-acetyl-alpha-neuraminic acid-(2-3)]beta-D-galactopyranose-(1-4)-beta-D-glucopyranose	K, N, O, P, S K, N, O, P, S, T	6		N/A	Interactions Focus chain K Focus chain N Focus chain O Focus chain P Focus chain S Focus chain T Interactions & Density Focus chain K Focus chain N Focus chain O Focus chain P Focus chain S Focus chain T
Glycosylation Resources
GlyTouCan: G91532KA GlyCosmos: G91532KA GlyGen: G91532KA

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose-(1-4)-[N-acetyl-alpha-neuraminic acid-(2-3)]beta-D-galactopyranose-(1-4)-beta-D-glucopyranose	L, R	7		N/A	Interactions Focus chain L Focus chain R Interactions & Density Focus chain L Focus chain R
Glycosylation Resources
GlyTouCan: G91532KA GlyCosmos: G91532KA GlyGen: G91532KA

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose-(1-4)-[N-acetyl-alpha-neuraminic acid-(2-3)]beta-D-galactopyranose-(1-4)-alpha-D-glucopyranose	M, Q	7		N/A	Interactions Focus chain M Focus chain Q Interactions & Density Focus chain M Focus chain Q
Glycosylation Resources
GlyTouCan: G18193SZ GlyCosmos: G18193SZ GlyGen: G18193SZ

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FUC Query on FUC Download Ideal Coordinates CCD File SDF format, chain OA [auth F] SDF format, chain PA [auth J] MOL2 format, chain OA [auth F] MOL2 format, chain PA [auth J]	OA [auth F], PA [auth J]	alpha-L-fucopyranose C₆ H₁₂ O₅ SHZGCJCMOBCMKK-SXUWKVJYSA-N		Interactions Focus chain OA [auth F] Focus chain PA [auth J] Interactions & Density Focus chain OA [auth F] Focus chain PA [auth J]
BCN Query on BCN Download Ideal Coordinates CCD File SDF format, chain BA [auth B] SDF format, chain CA [auth C] SDF format, chain EA [auth C] SDF format, chain GA [auth D] SDF format, chain JA [auth D] SDF format, chain KA [auth E] SDF format, chain MA [auth E] SDF format, chain V [auth A] SDF format, chain W [auth A] SDF format, chain Y [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain CA [auth C] MOL2 format, chain EA [auth C] MOL2 format, chain GA [auth D] MOL2 format, chain JA [auth D] MOL2 format, chain KA [auth E] MOL2 format, chain MA [auth E] MOL2 format, chain V [auth A] MOL2 format, chain W [auth A] MOL2 format, chain Y [auth B]	BA [auth B] CA [auth C] EA [auth C] GA [auth D] JA [auth D] BA [auth B], CA [auth C], EA [auth C], GA [auth D], JA [auth D], KA [auth E], MA [auth E], V [auth A], W [auth A], Y [auth B]	BICINE C₆ H₁₃ N O₄ FSVCELGFZIQNCK-UHFFFAOYSA-N		Interactions Focus chain BA [auth B] Focus chain CA [auth C] Focus chain EA [auth C] Focus chain GA [auth D] Focus chain JA [auth D] Focus chain KA [auth E] Focus chain MA [auth E] Focus chain V [auth A] Focus chain W [auth A] Focus chain Y [auth B] Interactions & Density Focus chain BA [auth B] Focus chain CA [auth C] Focus chain EA [auth C] Focus chain GA [auth D] Focus chain JA [auth D] Focus chain KA [auth E] Focus chain MA [auth E] Focus chain V [auth A] Focus chain W [auth A] Focus chain Y [auth B]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain DA [auth C] SDF format, chain FA [auth C] SDF format, chain HA [auth D] SDF format, chain IA [auth D] SDF format, chain LA [auth E] SDF format, chain NA [auth E] SDF format, chain U [auth A] SDF format, chain X [auth A] SDF format, chain Z [auth B] MOL2 format, chain AA [auth B] MOL2 format, chain DA [auth C] MOL2 format, chain FA [auth C] MOL2 format, chain HA [auth D] MOL2 format, chain IA [auth D] MOL2 format, chain LA [auth E] MOL2 format, chain NA [auth E] MOL2 format, chain U [auth A] MOL2 format, chain X [auth A] MOL2 format, chain Z [auth B]	AA [auth B] DA [auth C] FA [auth C] HA [auth D] IA [auth D] AA [auth B], DA [auth C], FA [auth C], HA [auth D], IA [auth D], LA [auth E], NA [auth E], U [auth A], X [auth A], Z [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain DA [auth C] Focus chain FA [auth C] Focus chain HA [auth D] Focus chain IA [auth D] Focus chain LA [auth E] Focus chain NA [auth E] Focus chain U [auth A] Focus chain X [auth A] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain DA [auth C] Focus chain FA [auth C] Focus chain HA [auth D] Focus chain IA [auth D] Focus chain LA [auth E] Focus chain NA [auth E] Focus chain U [auth A] Focus chain X [auth A] Focus chain Z [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.214
R-Value Work: 0.184
R-Value Observed: 0.185
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 148.626	α = 90
b = 74.137	β = 105.59
c = 111.245	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Coot	model building
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2019-08-14

Deposition Author(s):

Krengel, U.

Heim, J.B.

Funding Organization	Location	Grant Number
Research Council of Norway	Norway	247730

Revision History (Full details and data files)

Version 1.0: 2019-08-14
Type: Initial release
Version 1.1: 2019-10-02
Changes: Data collection, Database references
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Refinement description, Structure summary
Version 2.1: 2024-01-24
Changes: Data collection, Database references, Refinement description, Structure summary

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Help and Resources

6HMY

Cholera toxin classical B-pentamer in complex with fucosyl-GM1

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Entity ID: 2

Glycosylation Resources

Entity ID: 3

Glycosylation Resources

Entity ID: 4

Glycosylation Resources

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)