2HG1

N-Domain Of Grp94 In Complex With the Novel Ligand N-(2-hydroxyl)ethyl Carboxyamido Adenosine

PDB DOI: https://doi.org/10.2210/pdb2HG1/pdb

Classification: CHAPERONE
Organism(s): Canis lupus familiaris
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2006-06-26 Released: 2007-06-05
Deposition Author(s): Immormino, R.M., Gewirth, D.T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.243
R-Value Work: 0.214

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

N-Domain Of Grp94 In Complex With the Novel Ligand N-(2-hydroxyl)ethyl Carboxyamido Adenosine

Immormino, R.M., Gewirth, D.T.

To be published.

Macromolecule Content

Total Structure Weight: 55.49 kDa
Atom Count: 3,966
Modelled Residue Count: 451
Deposited Residue Count: 472
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endoplasmin	A, B	236	Canis lupus familiaris	Mutation(s): 0 Gene Names: HSP90B1, TRA1
UniProt
Find proteins for P41148 (Canis lupus familiaris) Explore P41148 Go to UniProtKB: P41148
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P41148
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
N5O Query on N5O Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain I [auth B] MOL2 format, chain C [auth A] MOL2 format, chain I [auth B] mmCIF format, chain C [auth A] mmCIF format, chain I [auth B]	C [auth A], I [auth B]	5'-N-(2-HYDROXYL)ETHYL CARBOXYAMIDO ADENOSINE C₁₂ H₁₆ N₆ O₅ YLPQAZPIFSHMAY-FLNNQWSLSA-N		Interactions Focus chain C [auth A] Focus chain I [auth B] Interactions & Density Focus chain C [auth A] Focus chain I [auth B]
1PE Query on 1PE Download Ideal Coordinates CCD File SDF format, chain N [auth B] MOL2 format, chain N [auth B] mmCIF format, chain N [auth B]	N [auth B]	PENTAETHYLENE GLYCOL C₁₀ H₂₂ O₆ JLFNLZLINWHATN-UHFFFAOYSA-N		Interactions Focus chain N [auth B] Interactions & Density Focus chain N [auth B]
PG4 Query on PG4 Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain M [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B]	D [auth A] E [auth A] F [auth A] G [auth A] J [auth B] D [auth A], E [auth A], F [auth A], G [auth A], J [auth B], K [auth B], L [auth B], M [auth B]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain H [auth B] MOL2 format, chain H [auth B] mmCIF format, chain H [auth B]	H [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain H [auth B] Interactions & Density Focus chain H [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.243
R-Value Work: 0.214
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.19	α = 90
b = 84.43	β = 90
c = 94.82	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
XDS	data reduction
XDS	data scaling
CNS	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2007-06-05

Deposition Author(s):

Immormino, R.M.

Gewirth, D.T.

Revision History (Full details and data files)

Version 1.0: 2007-06-05
Type: Initial release
Version 1.1: 2007-10-27
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2023-08-30
Changes: Data collection, Database references, Derived calculations, Refinement description