5C2K

Crystal structure of the fusion protein linked by RhoA and the GAP domain of MgcRacGAP

PDB DOI: https://doi.org/10.2210/pdb5C2K/pdb

Classification: HYDROLASE ACTIVATOR
Organism(s): Homo sapiens
Mutation(s): Yes

Deposited: 2015-06-16 Released: 2016-06-22
Deposition Author(s): Murayama, K., Kato-Murayama, M., Hosaka, T., Kitamura, T., Yokoyama, S., Shirouzu, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.42 Å
R-Value Free: 0.206
R-Value Work: 0.184
R-Value Observed: 0.184

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structural basis of G-protein target alternation of MgcRacGAP by phospholylation

Murayama, K., Kato-Murayama, M., Hosaka, T., kawashima, T., Kitamura, T., Yokoyama, S., Shirouzu, M.

To be published.

Macromolecule Content

Total Structure Weight: 46.62 kDa
Atom Count: 3,739
Modelled Residue Count: 382
Deposited Residue Count: 415
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transforming protein RhoA,Rac GTPase-activating protein 1	A	415	Homo sapiens	Mutation(s): 1 Gene Names: RHOA, RACGAP1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H0H5 (Homo sapiens) Explore Q9H0H5 Go to UniProtKB: Q9H0H5
PHAROS: Q9H0H5 GTEx: ENSG00000161800
Find proteins for P61586 (Homo sapiens) Explore P61586 Go to UniProtKB: P61586
PHAROS: P61586 GTEx: ENSG00000067560
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Groups	P61586Q9H0H5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GDP Query on GDP Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A]	D [auth A]	GUANOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₁ P₂ QGWNDRXFNXRZMB-UUOKFMHZSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
AF3 Query on AF3 Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	ALUMINUM FLUORIDE Al F₃ KLZUFWVZNOTSEM-UHFFFAOYSA-K		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.42 Å
R-Value Free: 0.206
R-Value Work: 0.184
R-Value Observed: 0.184
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.491	α = 90
b = 77.041	β = 108.53
c = 62.253	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2016-06-22

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2016-06-22
Type: Initial release
Version 1.1: 2020-02-19
Changes: Data collection, Derived calculations
Version 1.2: 2023-11-08
Changes: Data collection, Database references, Derived calculations, Refinement description

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Help and Resources

5C2K

Crystal structure of the fusion protein linked by RhoA and the GAP domain of MgcRacGAP

Structural basis of G-protein target alternation of MgcRacGAP by phospholylation

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)