4ADI

Crystal structure of the Rubella virus envelope glycoprotein E1 in post-fusion form (crystal form I)

PDB DOI: https://doi.org/10.2210/pdb4ADI/pdb

Classification: VIRAL PROTEIN
Organism(s): Rubella virus
Expression System: Drosophila melanogaster
Mutation(s): No

Deposited: 2011-12-26 Released: 2013-01-09
Deposition Author(s): DuBois, R.M., Vaney, M.C., Tortorici, M.A., Al Kurdi, R., Barba-Spaeth, G., Rey, F.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.183
R-Value Work: 0.167
R-Value Observed: 0.168

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 156.66 kDa
Atom Count: 11,662
Modelled Residue Count: 1,280
Deposited Residue Count: 1,419
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E1 ENVELOPE GLYCOPROTEIN	A, B, C	473	Rubella virus	Mutation(s): 0
UniProt
Find proteins for P08563 (Rubella virus (strain M33)) Explore P08563 Go to UniProtKB: P08563
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P08563
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NGA Query on NGA Download Ideal Coordinates CCD File SDF format, chain CA [auth B] SDF format, chain DA [auth B] SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain QA [auth C] SDF format, chain RA [auth C] MOL2 format, chain CA [auth B] MOL2 format, chain DA [auth B] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain QA [auth C] MOL2 format, chain RA [auth C]	CA [auth B] DA [auth B] P [auth A] Q [auth A] QA [auth C] CA [auth B], DA [auth B], P [auth A], Q [auth A], QA [auth C], RA [auth C]	2-acetamido-2-deoxy-beta-D-galactopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-JAJWTYFOSA-N		Interactions Focus chain CA [auth B] Focus chain DA [auth B] Focus chain P [auth A] Focus chain Q [auth A] Focus chain QA [auth C] Focus chain RA [auth C] Interactions & Density Focus chain CA [auth B] Focus chain DA [auth B] Focus chain P [auth A] Focus chain Q [auth A] Focus chain QA [auth C] Focus chain RA [auth C]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain BA [auth B] SDF format, chain D [auth A] SDF format, chain EA [auth C] SDF format, chain O [auth A] SDF format, chain PA [auth C] SDF format, chain R [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain D [auth A] MOL2 format, chain EA [auth C] MOL2 format, chain O [auth A] MOL2 format, chain PA [auth C] MOL2 format, chain R [auth B]	BA [auth B] D [auth A] EA [auth C] O [auth A] PA [auth C] BA [auth B], D [auth A], EA [auth C], O [auth A], PA [auth C], R [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain BA [auth B] Focus chain D [auth A] Focus chain EA [auth C] Focus chain O [auth A] Focus chain PA [auth C] Focus chain R [auth B] Interactions & Density Focus chain BA [auth B] Focus chain D [auth A] Focus chain EA [auth C] Focus chain O [auth A] Focus chain PA [auth C] Focus chain R [auth B]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain N [auth A] SDF format, chain NA [auth C] SDF format, chain OA [auth C] MOL2 format, chain AA [auth B] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth C] MOL2 format, chain OA [auth C]	AA [auth B], N [auth A], NA [auth C], OA [auth C]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain N [auth A] Focus chain NA [auth C] Focus chain OA [auth C] Interactions & Density Focus chain AA [auth B] Focus chain N [auth A] Focus chain NA [auth C] Focus chain OA [auth C]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain FA [auth C] SDF format, chain G [auth A] SDF format, chain GA [auth C] SDF format, chain H [auth A] SDF format, chain HA [auth C] SDF format, chain I [auth A] SDF format, chain IA [auth C] SDF format, chain J [auth A] SDF format, chain JA [auth C] SDF format, chain KA [auth C] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain U [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain FA [auth C] MOL2 format, chain G [auth A] MOL2 format, chain GA [auth C] MOL2 format, chain H [auth A] MOL2 format, chain HA [auth C] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth C] MOL2 format, chain J [auth A] MOL2 format, chain JA [auth C] MOL2 format, chain KA [auth C] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B]	E [auth A] F [auth A] FA [auth C] G [auth A] GA [auth C] E [auth A], F [auth A], FA [auth C], G [auth A], GA [auth C], H [auth A], HA [auth C], I [auth A], IA [auth C], J [auth A], JA [auth C], KA [auth C], S [auth B], T [auth B], U [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain FA [auth C] Focus chain G [auth A] Focus chain GA [auth C] Focus chain H [auth A] Focus chain HA [auth C] Focus chain I [auth A] Focus chain IA [auth C] Focus chain J [auth A] Focus chain JA [auth C] Focus chain KA [auth C] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain FA [auth C] Focus chain G [auth A] Focus chain GA [auth C] Focus chain H [auth A] Focus chain HA [auth C] Focus chain I [auth A] Focus chain IA [auth C] Focus chain J [auth A] Focus chain JA [auth C] Focus chain KA [auth C] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain MA [auth C] SDF format, chain W [auth B] SDF format, chain X [auth B] SDF format, chain Y [auth B] SDF format, chain Z [auth B] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth C] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B]	L [auth A] M [auth A] MA [auth C] W [auth B] X [auth B] L [auth A], M [auth A], MA [auth C], W [auth B], X [auth B], Y [auth B], Z [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain L [auth A] Focus chain M [auth A] Focus chain MA [auth C] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain L [auth A] Focus chain M [auth A] Focus chain MA [auth C] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain LA [auth C] SDF format, chain V [auth B] MOL2 format, chain K [auth A] MOL2 format, chain LA [auth C] MOL2 format, chain V [auth B]	K [auth A], LA [auth C], V [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain LA [auth C] Focus chain V [auth B] Interactions & Density Focus chain K [auth A] Focus chain LA [auth C] Focus chain V [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.183
R-Value Work: 0.167
R-Value Observed: 0.168
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 129.98	α = 90
b = 121.38	β = 90
c = 126.43	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
SCALA	data scaling
SHARP	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2013-01-09

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-01-09
Type: Initial release
Version 1.1: 2013-01-23
Changes: Database references
Version 1.2: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Other, Structure summary