2C5C | pdb_00002c5c

Shiga-like toxin 1 B subunit complexed with a bivalent inhibitor

PDB DOI: https://doi.org/10.2210/pdb2C5C/pdb

Classification: TOXIN
Organism(s): Phage h30
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2005-10-26 Released: 2006-11-27
Deposition Author(s): Dodd, R.B., Read, R.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.94 Å
R-Value Free:
0.267 (Depositor), 0.277 (DCC)
R-Value Work:
0.198 (Depositor), 0.205 (DCC)
R-Value Observed:
0.201 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 3.2 of the entry. See complete history.

Literature

Extensive Cross-Linking of the Shiga-Like Toxin 1 B Subunit by a Bivalent Ligand

Dodd, R.B., Read, R.J.

To be published.

Macromolecule Content

Total Structure Weight: 88.12 kDa
Atom Count: 6,136
Modeled Residue Count: 690
Deposited Residue Count: 690
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SHIGA-LIKE TOXIN 1 B SUBUNIT	A, B, C, D, E A, B, C, D, E, F, G, H, I, J	69	Phage h30	Mutation(s): 0
UniProt
Find proteins for P69178 (Bacteriophage H30) Explore P69178 Go to UniProtKB: P69178
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P69178
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-galactopyranose-(1-4)-beta-D-galactopyranose-(1-4)-alpha-D-glucopyranose	CA [auth c], DA [auth d], K, L, M, CA [auth c], DA [auth d], K, L, M, N, O, Q, V, Y	3		N/A	Interactions Focus chain CA [auth c] Focus chain DA [auth d] Focus chain K Focus chain L Focus chain M Focus chain N Focus chain O Focus chain Q Focus chain V Focus chain Y Interactions & Density Focus chain CA [auth c] Focus chain DA [auth d] Focus chain K Focus chain L Focus chain M Focus chain N Focus chain O Focus chain Q Focus chain V Focus chain Y
Glycosylation Resources
GlyTouCan: G79094AA GlyCosmos: G79094AA GlyGen: G79094AA

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-galactopyranose-(1-4)-alpha-D-galactopyranose	P, R, U, W, X P, R, U, W, X, Z	2		N/A	Interactions Focus chain P Focus chain R Focus chain U Focus chain W Focus chain X Focus chain Z Interactions & Density Focus chain P Focus chain R Focus chain U Focus chain W Focus chain X Focus chain Z
Glycosylation Resources
GlyTouCan: G54046EC GlyCosmos: G54046EC GlyGen: G54046EC

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-galactopyranose-(1-4)-beta-D-galactopyranose-(1-4)-beta-D-glucopyranose	S, T	3		N/A	Interactions Focus chain S Focus chain T Interactions & Density Focus chain S Focus chain T
Glycosylation Resources
GlyTouCan: G00059MO GlyCosmos: G00059MO GlyGen: G00059MO

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-galactopyranose-(1-4)-alpha-D-galactopyranose-(1-4)-beta-D-glucopyranose	AA [auth a], BA [auth b]	3		N/A	Interactions Focus chain AA [auth a] Focus chain BA [auth b] Interactions & Density Focus chain AA [auth a] Focus chain BA [auth b]
Glycosylation Resources
GlyTouCan: G80589WZ GlyCosmos: G80589WZ GlyGen: G80589WZ

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
S10 Query on S10 Download:Ideal Coordinates CCD File SDF format, chain EA [auth A] SDF format, chain GA [auth C] SDF format, chain HA [auth D] SDF format, chain IA [auth E] SDF format, chain JA [auth F] SDF format, chain KA [auth I] SDF format, chain MA [auth J] SDF format, chain NA [auth J] MOL2 format, chain EA [auth A] MOL2 format, chain GA [auth C] MOL2 format, chain HA [auth D] MOL2 format, chain IA [auth E] MOL2 format, chain JA [auth F] MOL2 format, chain KA [auth I] MOL2 format, chain MA [auth J] MOL2 format, chain NA [auth J] mmCIF format, chain EA [auth A] mmCIF format, chain GA [auth C] mmCIF format, chain HA [auth D] mmCIF format, chain IA [auth E] mmCIF format, chain JA [auth F] mmCIF format, chain KA [auth I] mmCIF format, chain MA [auth J] mmCIF format, chain NA [auth J]	EA [auth A] GA [auth C] HA [auth D] IA [auth E] JA [auth F] EA [auth A], GA [auth C], HA [auth D], IA [auth E], JA [auth F], KA [auth I], MA [auth J], NA [auth J]	DIETHYL PROPANE-1,3-DIYLBISCARBAMATE C₉ H₁₈ N₂ O₄ BWWHOVJFNMPUKF-UHFFFAOYSA-N		Interactions Focus chain EA [auth A] Focus chain GA [auth C] Focus chain HA [auth D] Focus chain IA [auth E] Focus chain JA [auth F] Focus chain KA [auth I] Focus chain MA [auth J] Focus chain NA [auth J] Interactions & Density Focus chain EA [auth A] Focus chain GA [auth C] Focus chain HA [auth D] Focus chain IA [auth E] Focus chain JA [auth F] Focus chain KA [auth I] Focus chain MA [auth J] Focus chain NA [auth J]
GLA Query on GLA Download:Ideal Coordinates CCD File SDF format, chain FA [auth C] MOL2 format, chain FA [auth C] mmCIF format, chain FA [auth C]	FA [auth C]	alpha-D-galactopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-PHYPRBDBSA-N		Interactions Focus chain FA [auth C] Interactions & Density Focus chain FA [auth C]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain LA [auth I] MOL2 format, chain LA [auth I] mmCIF format, chain LA [auth I]	LA [auth I]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain LA [auth I] Interactions & Density Focus chain LA [auth I]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.94 Å
R-Value Free: 0.267 (Depositor), 0.277 (DCC)
R-Value Work: 0.198 (Depositor), 0.205 (DCC)
R-Value Observed: 0.201 (Depositor)

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 114.313	α = 90
b = 114.313	β = 90
c = 406.936	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
AMoRE	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2006-11-27

Deposition Author(s):

Dodd, R.B.

Read, R.J.

Revision History (Full details and data files)

Version 1.0: 2006-11-27
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 2.0: 2018-12-19
Changes: Advisory, Atomic model, Data collection, Derived calculations
Version 2.1: 2020-07-01
Changes: Data collection, Other
Version 3.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
Version 3.1: 2023-12-13
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
Version 3.2: 2024-11-13
Changes: Structure summary