5WFU | pdb_00005wfu

Structural basis for the interaction of 14-3-3beta with Tricarboxylic Acid Cycle intermediate Malate

PDB DOI: https://doi.org/10.2210/pdb5WFU/pdb

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

Deposited: 2017-07-12 Released: 2018-07-18
Deposition Author(s): Hou, Z.Q., Liu, X.Y.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.97 Å
R-Value Free:
0.224 (Depositor), 0.233 (DCC)
R-Value Work:
0.190 (Depositor), 0.198 (DCC)
R-Value Observed:
0.192 (Depositor)

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Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Structural basis for the interaction of 14-3-3beta with Tricarboxylic Acid Cycle intermediate Malate

Hou, Z.Q., Su, L.J., Liu, X.Y.

To be published.

Macromolecule Content

Total Structure Weight: 113.01 kDa
Atom Count: 7,865
Modeled Residue Count: 934
Deposited Residue Count: 984
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
14-3-3 protein beta/alpha	A, B, C, D	246	Mus musculus	Mutation(s): 0 Gene Names: Ywhab
UniProt & NIH Common Fund Data Resources
Find proteins for Q9CQV8 (Mus musculus) Explore Q9CQV8 Go to UniProtKB: Q9CQV8
IMPC: MGI:1891917
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9CQV8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MLT (Subject of Investigation/LOI) Query on MLT Download:Ideal Coordinates CCD File SDF format, chain H [auth D] SDF format, chain G [auth C] SDF format, chain F [auth B] SDF format, chain E [auth A] MOL2 format, chain H [auth D] MOL2 format, chain G [auth C] MOL2 format, chain F [auth B] MOL2 format, chain E [auth A] mmCIF format, chain H [auth D] mmCIF format, chain G [auth C] mmCIF format, chain F [auth B] mmCIF format, chain E [auth A]	E [auth A], F [auth B], G [auth C], H [auth D]	D-MALATE C₄ H₆ O₅ BJEPYKJPYRNKOW-UWTATZPHSA-N		Interactions Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.97 Å
R-Value Free: 0.224 (Depositor), 0.233 (DCC)
R-Value Work: 0.190 (Depositor), 0.198 (DCC)
R-Value Observed: 0.192 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 256.392	α = 90
b = 85.604	β = 101.73
c = 56.066	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
PHENIX	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2018-07-18

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2018-07-18
Type: Initial release
Version 1.1: 2024-03-13
Changes: Data collection, Database references, Refinement description

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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.