5I6R | pdb_00005i6r

Crystal Structure of srGAP2 F-BARx WT Form-1

PDB DOI: https://doi.org/10.2210/pdb5I6R/pdb

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

Deposited: 2016-02-16 Released: 2017-08-30
Deposition Author(s): Sporny, M., Guez-Haddad, J., Isupov, M.N., Opatowsky, Y.
Funding Organization(s): ISF, BSF

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free:
0.260 (Depositor), 0.260 (DCC)
R-Value Work:
0.203 (Depositor), 0.203 (DCC)
R-Value Observed:
0.206 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 5I6R

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

Literature

Structural Basis for srGAP2 Membrane Interactions, and Antagonism by the Human Specific Paralog srGAP2C

Sporny, M., Guez-Haddad, J., Isupov, M.N., Opatowsky, Y.

To be published.

Macromolecule Content

Total Structure Weight: 57.02 kDa
Atom Count: 3,932
Modeled Residue Count: 419
Deposited Residue Count: 484
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SLIT-ROBO Rho GTPase-activating protein 2	A	484	Homo sapiens	Mutation(s): 1 Gene Names: SRGAP2, ARHGAP34, FNBP2, KIAA0456, SRGAP2A
UniProt & NIH Common Fund Data Resources
Find proteins for O75044 (Homo sapiens) Explore O75044 Go to UniProtKB: O75044
PHAROS: O75044 GTEx: ENSG00000266028
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O75044
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PGE Query on PGE 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]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
MLT Query on MLT Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	D-MALATE C₄ H₆ O₅ BJEPYKJPYRNKOW-UWTATZPHSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A]	C [auth A], D [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.260 (Depositor), 0.260 (DCC)
R-Value Work: 0.203 (Depositor), 0.203 (DCC)
R-Value Observed: 0.206 (Depositor)

Space Group: P 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.3	α = 90
b = 29.76	β = 92.99
c = 94.63	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
MOLREP	phasing

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2017-08-30

Deposition Author(s):

Guez-Haddad, J.

Funding Organization	Location	Grant Number
ISF	Israel	182/10 and 1425/15
BSF	Israel	2013310

Revision History (Full details and data files)

Version 1.0: 2017-08-30
Type: Initial release
Version 1.1: 2019-10-16
Changes: Data collection
Version 1.2: 2024-05-08
Changes: Data collection, Database references

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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.