2GQP | pdb_00002gqp

N-Domain Of Grp94 In Complex With the Novel Ligand N-Propyl Carboxyamido Adenosine

PDB DOI: https://doi.org/10.2210/pdb2GQP/pdb

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

Deposited: 2006-04-21 Released: 2007-04-03
Deposition Author(s): Immormino, R.M., Gewirth, D.T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free:
0.235 (Depositor), 0.251 (DCC)
R-Value Work:
0.215 (Depositor), 0.230 (DCC)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Adensine Scaffold inhibitors of GRP94

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

To be published.

Macromolecule Content

Total Structure Weight: 55.29 kDa
Atom Count: 4,177
Modeled Residue Count: 418
Deposited Residue Count: 472
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 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 EC: 3.6.4
UniProt
Find proteins for P41148 (Canis lupus familiaris) Explore P41148 Go to UniProtKB: P41148
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P41148
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PA7 Query on PA7 Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain I [auth B] MOL2 format, chain D [auth A] MOL2 format, chain I [auth B] mmCIF format, chain D [auth A] mmCIF format, chain I [auth B]	D [auth A], I [auth B]	N-PROPYL CARBOXYAMIDO ADENOSINE C₁₃ H₁₈ N₆ O₄ UQGKLARJCHZHSS-QRIDJOKKSA-N		Interactions Focus chain D [auth A] Focus chain I [auth B] Interactions & Density Focus chain D [auth A] Focus chain I [auth B]
1PE Query on 1PE Download:Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	PENTAETHYLENE GLYCOL C₁₀ H₂₂ O₆ JLFNLZLINWHATN-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
PG4 Query on PG4 Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain K [auth B] SDF format, chain M [auth B] SDF format, chain L [auth B] SDF format, chain J [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain K [auth B] MOL2 format, chain M [auth B] MOL2 format, chain L [auth B] MOL2 format, chain J [auth B] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain K [auth B] mmCIF format, chain M [auth B] mmCIF format, chain L [auth B] mmCIF format, chain J [auth B]	E [auth A] F [auth A] G [auth A] J [auth B] K [auth B] 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 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 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 C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.235 (Depositor), 0.251 (DCC)
R-Value Work: 0.215 (Depositor), 0.230 (DCC)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.69	α = 90
b = 84.84	β = 90
c = 95.74	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
XDS	data scaling
MOLREP	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2007-04-03

Deposition Author(s):

Immormino, R.M.

Gewirth, D.T.

Revision History (Full details and data files)

Version 1.0: 2007-04-03
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: 2017-08-02
Changes: Advisory, Source and taxonomy
Version 1.4: 2023-08-30
Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description

2GQP | pdb_00002gqp

N-Domain Of Grp94 In Complex With the Novel Ligand N-Propyl Carboxyamido Adenosine

Literature

Adensine Scaffold inhibitors of GRP94

Biological Assembly 1

Biological Assembly 2

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand