6FCJ | pdb_00006fcj

Estimation of Protein-Ligand Unbinding Kinetics Using Non-Equilibrium Targeted Molecular Dynamics Simulations

PDB DOI: https://doi.org/10.2210/pdb6FCJ/pdb

Classification: CHAPERONE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2017-12-20 Released: 2019-01-30
Deposition Author(s): Musil, D., Lehmann, M., Eggenweiler, H.-M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.49 Å
R-Value Free:
0.234 (Depositor), 0.230 (DCC)
R-Value Work:
0.188 (Depositor), 0.192 (DCC)
R-Value Observed:
0.190 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 6FCJ

Ligand Structure Quality Assessment

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

Literature

Estimation of Protein-Ligand Unbinding Kinetics Using Non-Equilibrium Targeted Molecular Dynamics Simulations

Wolf, S., Amaral, M., Lowinski, M., Vallee, F., Musil, D., Guldenhaupt, J., Dreyer, M.K., Bomke, J., Frech, M., Schlitter, J., Gerwert, K.

(2019) ArXiv

Macromolecule Content

Total Structure Weight: 26 kDa
Atom Count: 1,715
Modeled Residue Count: 208
Deposited Residue Count: 229
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Heat shock protein HSP 90-alpha	A	229	Homo sapiens	Mutation(s): 0 Gene Names: HSP90AA1, HSP90A, HSPC1, HSPCA EC: 3.6.4.10
UniProt & NIH Common Fund Data Resources
Find proteins for P07900 (Homo sapiens) Explore P07900 Go to UniProtKB: P07900
PHAROS: P07900 GTEx: ENSG00000080824
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P07900
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
D4W Query on D4W Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	4-[2-(2-chlorophenyl)pyrazol-3-yl]benzene-1,3-diol C₁₅ H₁₁ Cl N₂ O₂ NXZPXDLYOVGQMR-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.49 Å
R-Value Free: 0.234 (Depositor), 0.230 (DCC)
R-Value Work: 0.188 (Depositor), 0.192 (DCC)
R-Value Observed: 0.190 (Depositor)

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.015	α = 90
b = 89.814	β = 90
c = 98.47	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
BUSTER	refinement
PDB_EXTRACT	data extraction
DENZO	data reduction
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2019-01-30

Deposition Author(s):

Eggenweiler, H.-M.

Revision History (Full details and data files)

Version 1.0: 2019-01-30
Type: Initial release
Version 1.1: 2019-08-14
Changes: Data collection, Database references, Structure summary
Version 1.2: 2024-05-08
Changes: Data collection, Database references

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.