5NAS | pdb_00005nas

Crystal structure of human 14-3-3 zeta in complex with PI4KIIIB peptide

PDB DOI: https://doi.org/10.2210/pdb5NAS/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2017-02-28 Released: 2017-03-29
Deposition Author(s): Boura, E., Eisenreichova, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.08 Å
R-Value Free:
0.231 (Depositor), 0.236 (DCC)
R-Value Work:
0.188 (Depositor), 0.199 (DCC)
R-Value Observed:
0.190 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of human 14-3-3 zeta in complex with PI4KIIIB peptide

Boura, E., Eisenreichova, A.

To be published.

Macromolecule Content

Total Structure Weight: 55.08 kDa
Atom Count: 4,029
Modeled Residue Count: 476
Deposited Residue Count: 482
Unique protein chains: 2

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
14-3-3 protein zeta/delta	A, B	232	Homo sapiens	Mutation(s): 0 Gene Names: YWHAZ
UniProt & NIH Common Fund Data Resources
Find proteins for P63104 (Homo sapiens) Explore P63104 Go to UniProtKB: P63104
PHAROS: P63104 GTEx: ENSG00000164924
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P63104
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphatidylinositol 4-kinase beta	C, D	9	Homo sapiens	Mutation(s): 0 EC: 2.7.1.67
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UBF8 (Homo sapiens) Explore Q9UBF8 Go to UniProtKB: Q9UBF8
PHAROS: Q9UBF8 GTEx: ENSG00000143393
Entity Groups
UniProt Group	Q9UBF8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEP Query on SEP	C, D	L-PEPTIDE LINKING	C₃ H₈ N O₆ P		SER

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.08 Å
R-Value Free: 0.231 (Depositor), 0.236 (DCC)
R-Value Work: 0.188 (Depositor), 0.199 (DCC)
R-Value Observed: 0.190 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.822	α = 90
b = 83.553	β = 90
c = 111.538	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2017-03-29

Deposition Author(s):

Eisenreichova, A.

Revision History (Full details and data files)

Version 1.0: 2017-03-29
Type: Initial release
Version 1.1: 2024-01-17
Changes: Data collection, Database references, Refinement description
Version 1.2: 2024-10-09
Changes: Structure summary

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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.