2DWZ | pdb_00002dwz

Structure of the Oncoprotein Gankyrin in Complex with S6 ATPase of the 26S Proteasome

PDB DOI: https://doi.org/10.2210/pdb2DWZ/pdb

Classification: ONCOPROTEIN
Organism(s): Mus musculus, Rattus norvegicus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2006-08-22 Released: 2007-08-28
Deposition Author(s): Padmanabhan, B., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.268 (Depositor)
R-Value Work:
0.194 (Depositor)
R-Value Observed:
0.194 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Structure of the Oncoprotein Gankyrin in Complex with S6 ATPase of the 26S Proteasome

Nakamura, Y., Nakano, K., Umehara, T., Tanaka, A., Padmanabhan, B., Yokoyama, S.

To be published.

Macromolecule Content

Total Structure Weight: 70 kDa
Atom Count: 4,864
Modeled Residue Count: 598
Deposited Residue Count: 628
Unique protein chains: 2

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
26S proteasome non-ATPase regulatory subunit 10	A, C	231	Mus musculus	Mutation(s): 0
UniProt
Find proteins for Q9Z2X2 (Mus musculus) Explore Q9Z2X2 Go to UniProtKB: Q9Z2X2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9Z2X2
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
26S protease regulatory subunit 6B	B, D	83	Rattus norvegicus	Mutation(s): 0
UniProt
Find proteins for Q63570 (Rattus norvegicus) Explore Q63570 Go to UniProtKB: Q63570
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q63570
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EPE Query on EPE Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C₈ H₁₈ N₂ O₄ S JKMHFZQWWAIEOD-UHFFFAOYSA-N		Interactions Focus chain E [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.268 (Depositor)
R-Value Work: 0.194 (Depositor)
R-Value Observed: 0.194 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.991	α = 90
b = 92.319	β = 90
c = 167.191	γ = 90

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2007-08-28

Deposition Author(s):

Padmanabhan, B.

RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History (Full details and data files)

Version 1.0: 2007-08-28
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2024-03-13
Changes: Data collection, Database references, Derived calculations

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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.