2HCH | pdb_00002hch

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

PDB DOI: https://doi.org/10.2210/pdb2HCH/pdb

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

Deposited: 2006-06-16 Released: 2007-05-01
Deposition Author(s): Immormino, R.M., Gewirth, D.T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.254 (Depositor), 0.262 (DCC)
R-Value Work:
0.220 (Depositor), 0.227 (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

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

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

To be published.

Macromolecule Content

Total Structure Weight: 54.88 kDa
Atom Count: 3,825
Modeled Residue Count: 439
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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
N5A Query on N5A Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain G [auth B] MOL2 format, chain C [auth A] MOL2 format, chain G [auth B] mmCIF format, chain C [auth A] mmCIF format, chain G [auth B]	C [auth A], G [auth B]	5'-N-[(2-AMINO)ETHYL CARBOXAMIDO] ADENOSINE C₁₂ H₁₇ N₇ O₄ XZUQLQNOMFGRFJ-FLNNQWSLSA-N		Interactions Focus chain C [auth A] Focus chain G [auth B] Interactions & Density Focus chain C [auth A] Focus chain G [auth B]
1PE Query on 1PE Download:Ideal Coordinates CCD File SDF format, chain J [auth B] MOL2 format, chain J [auth B] mmCIF format, chain J [auth B]	J [auth B]	PENTAETHYLENE GLYCOL C₁₀ H₂₂ O₆ JLFNLZLINWHATN-UHFFFAOYSA-N		Interactions Focus chain J [auth B] Interactions & Density Focus chain J [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 H [auth B] SDF format, chain I [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B]	D [auth A], E [auth A], F [auth A], H [auth B], I [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 H [auth B] Focus chain I [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.254 (Depositor), 0.262 (DCC)
R-Value Work: 0.220 (Depositor), 0.227 (DCC)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.66	α = 90
b = 84.77	β = 90
c = 94.92	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
CNS	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2007-05-01

Deposition Author(s):

Immormino, R.M.

Gewirth, D.T.

Revision History (Full details and data files)

Version 1.0: 2007-05-01
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2017-08-02
Changes: Source and taxonomy
Version 1.4: 2023-08-30
Changes: Data collection, Database references, Derived calculations, Refinement description

2HCH | pdb_00002hch

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

Literature

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

Biological Assembly 1

Biological Assembly 2

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand