2Z17 | pdb_00002z17

Crystal structure of PDZ domain from human Pleckstrin homology, Sec7

PDB DOI: https://doi.org/10.2210/pdb2Z17/pdb

Classification: PROTEIN BINDING
Organism(s): Homo sapiens
Mutation(s): No

Deposited: 2007-05-08 Released: 2008-05-13
Deposition Author(s): Kishishita, S., Nishino, A., Murayama, K., Terada, T., Shirouzu, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free:
0.334 (Depositor), 0.346 (DCC)
R-Value Work:
0.244 (Depositor), 0.261 (DCC)
R-Value Observed:
0.244 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 2Z17

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

Literature

Crystal structure of PDZ domain from human Pleckstrin homology, Sec7

Kishishita, S., Nishino, A., Murayama, K., Terada, T., Shirouzu, M., Yokoyama, S.

To be published.

Macromolecule Content

Total Structure Weight: 11.3 kDa
Atom Count: 745
Modeled Residue Count: 94
Deposited Residue Count: 104
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pleckstrin homology Sec7 and coiled-coil domains-binding protein	A	104	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for O60759 (Homo sapiens) Explore O60759 Go to UniProtKB: O60759
PHAROS: O60759 GTEx: ENSG00000115165
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O60759
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.334 (Depositor), 0.346 (DCC)
R-Value Work: 0.244 (Depositor), 0.261 (DCC)
R-Value Observed: 0.244 (Depositor)

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.917	α = 90
b = 65.917	β = 90
c = 81.09	γ = 120

Software Package:

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

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2008-05-13

Deposition Author(s):

RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History (Full details and data files)

Version 1.0: 2008-05-13
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2020-09-09
Changes: Database references, Structure summary
Version 1.3: 2024-03-13
Changes: Data collection, Database references

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.