4TZC | pdb_00004tzc

Crystal Structure of Murine Cereblon in Complex with Thalidomide

PDB DOI: https://doi.org/10.2210/pdb4TZC/pdb

Classification: LIGASE
Organism(s): Mus musculus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2014-07-10 Released: 2014-08-06
Deposition Author(s): Chamberlain, P.P., Pagarigan, B., Delker, S., Leon, B.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.88 Å
R-Value Free:
0.220 (Depositor), 0.220 (DCC)
R-Value Work:
0.173 (Depositor), 0.170 (DCC)
R-Value Observed:
0.175 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structural Basis for Responsiveness to Thalidomide-Analog Drugs Defined by the Crystal Structure of the Human Cereblon:DDB1:Lenalidomide Complex

Chamberlain, P.P., Lopez-Girona, A., Miller, K., Carmel, G., Pagarigan, B., Leon, B., Rychak, E., Corral, L., Ren, Y., Wang, M., Riley, M., Delker, S., Ito, T., Hideki, A., Mori, T., Hirano, Y., Handa, H., Hakoshima, T., Daniel, T.O., Cathers, B.E.

To be published.

Macromolecule Content

Total Structure Weight: 50.29 kDa
Atom Count: 3,578
Modelled Residue Count: 391
Deposited Residue Count: 432
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein cereblon	A [auth C], B [auth A], C [auth B], D	108	Mus musculus	Mutation(s): 0 Gene Names: Crbn
UniProt & NIH Common Fund Data Resources
Find proteins for Q8C7D2 (Mus musculus) Explore Q8C7D2 Go to UniProtKB: Q8C7D2
IMPC: MGI:1913277
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8C7D2
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EF2 Query on EF2 Download Ideal Coordinates CCD File SDF format, chain F [auth C] SDF format, chain J [auth A] SDF format, chain O [auth B] SDF format, chain T [auth D] MOL2 format, chain F [auth C] MOL2 format, chain J [auth A] MOL2 format, chain O [auth B] MOL2 format, chain T [auth D] mmCIF format, chain F [auth C] mmCIF format, chain J [auth A] mmCIF format, chain O [auth B] mmCIF format, chain T [auth D]	F [auth C], J [auth A], O [auth B], T [auth D]	S-Thalidomide C₁₃ H₁₀ N₂ O₄ UEJJHQNACJXSKW-VIFPVBQESA-N		Interactions Focus chain F [auth C] Focus chain J [auth A] Focus chain O [auth B] Focus chain T [auth D] Interactions & Density Focus chain F [auth C] Focus chain J [auth A] Focus chain O [auth B] Focus chain T [auth D]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain Q [auth D] SDF format, chain R [auth D] SDF format, chain S [auth D] SDF format, chain L [auth B] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain Q [auth D] MOL2 format, chain R [auth D] MOL2 format, chain S [auth D] MOL2 format, chain L [auth B] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain Q [auth D] mmCIF format, chain R [auth D] mmCIF format, chain S [auth D] mmCIF format, chain L [auth B]	H [auth A] I [auth A] L [auth B] M [auth B] N [auth B] H [auth A], I [auth A], L [auth B], M [auth B], N [auth B], Q [auth D], R [auth D], S [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain Q [auth D] Focus chain R [auth D] Focus chain S [auth D] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain Q [auth D] Focus chain R [auth D] Focus chain S [auth D]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain K [auth B] SDF format, chain P [auth D] SDF format, chain E [auth C] MOL2 format, chain G [auth A] MOL2 format, chain K [auth B] MOL2 format, chain P [auth D] MOL2 format, chain E [auth C] mmCIF format, chain G [auth A] mmCIF format, chain K [auth B] mmCIF format, chain P [auth D] mmCIF format, chain E [auth C]	E [auth C], G [auth A], K [auth B], P [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain E [auth C] Focus chain G [auth A] Focus chain K [auth B] Focus chain P [auth D] Interactions & Density Focus chain E [auth C] Focus chain G [auth A] Focus chain K [auth B] Focus chain P [auth D]

Binding Affinity Annotations
ID	Source	Binding Affinity
EF2	BindingDB: 4TZC	Ki: min: 1800, max: 2.27e+4 (nM) from 5 assay(s)
EF2	BindingDB: 4TZC	IC50: min: 268, max: 2.99e+4 (nM) from 7 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.88 Å
R-Value Free: 0.220 (Depositor), 0.220 (DCC)
R-Value Work: 0.173 (Depositor), 0.170 (DCC)
R-Value Observed: 0.175 (Depositor)

Space Group: I 2 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 143.146	α = 90
b = 143.146	β = 90
c = 143.146	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
PDB_EXTRACT	data extraction
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2014-08-06

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-08-06
Type: Initial release
Version 1.1: 2016-03-16
Changes: Data collection
Version 1.2: 2017-09-27
Changes: Derived calculations, Refinement description
Version 1.3: 2023-12-27
Changes: Data collection, Database references