1U5D | pdb_00001u5d

Crystal Structure of the PH domain of SKAP55

PDB DOI: https://doi.org/10.2210/pdb1U5D/pdb

Classification: SIGNALING PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes
Membrane Protein: Yes OPM

Deposited: 2004-07-27 Released: 2005-07-26
Deposition Author(s): Tang, Y., Swanson, K.D., Neel, B.G., Eck, M.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.185 (Depositor), 0.218 (DCC)
R-Value Work:
0.168 (Depositor), 0.183 (DCC)
R-Value Observed:
0.168 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 1U5D

This is version 1.4 of the entry. See complete history.

Literature

Structural Basis for the Dimerization and Phosphoinositide Specificity of the Src Kinase-associated Phosphoproteins SKAP55 and SKAP-Hom

Tang, Y., Swanson, K.D., Neel, B.G., Eck, M.J.

To be published.

Macromolecule Content

Total Structure Weight: 51.57 kDa
Atom Count: 4,040
Modeled Residue Count: 430
Deposited Residue Count: 432
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Src Kinase-associated Phosphoprotein of 55 kDa	A, B, C, D	108	Homo sapiens	Mutation(s): 2 Gene Names: HSSKAP55 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q86WV1 (Homo sapiens) Explore Q86WV1 Go to UniProtKB: Q86WV1
PHAROS: Q86WV1 GTEx: ENSG00000141293
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q86WV1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain K [auth D] SDF format, chain J [auth D] SDF format, chain I [auth C] SDF format, chain H [auth C] SDF format, chain G [auth B] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain K [auth D] MOL2 format, chain J [auth D] MOL2 format, chain I [auth C] MOL2 format, chain H [auth C] MOL2 format, chain G [auth B] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain K [auth D] mmCIF format, chain J [auth D] mmCIF format, chain I [auth C] mmCIF format, chain H [auth C] mmCIF format, chain G [auth B] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A] F [auth A] G [auth B] H [auth C] I [auth C] E [auth A], F [auth A], G [auth B], H [auth C], I [auth C], J [auth D], K [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth B] Focus chain H [auth C] Focus chain I [auth C] Focus chain J [auth D] Focus chain K [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth B] Focus chain H [auth C] Focus chain I [auth C] Focus chain J [auth D] Focus chain K [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.185 (Depositor), 0.218 (DCC)
R-Value Work: 0.168 (Depositor), 0.183 (DCC)
R-Value Observed: 0.168 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.068	α = 90
b = 33.352	β = 110.31
c = 105.382	γ = 90

Software Package:

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

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2005-07-26

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2005-07-26
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2021-10-20
Changes: Database references, Derived calculations
Version 1.4: 2023-08-23
Changes: Data collection, 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.