2QME | pdb_00002qme

Crystal structure of human RAC3 in complex with CRIB domain of human p21-activated kinase 1 (PAK1)

PDB DOI: https://doi.org/10.2210/pdb2QME/pdb

Classification: SIGNALING PROTEIN/TRANSFERASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2007-07-16 Released: 2007-08-28
Deposition Author(s): Ugochukwu, E., Yang, X., Elkins, J.M., Burgess-Brown, N., Bunkoczi, G., Sundstrom, M., Arrowsmith, C.H., Weigelt, J., Edwards, A., von Delft, F., Knapp, S., Doyle, D., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free:
0.192 (Depositor), 0.200 (DCC)
R-Value Work:
0.149 (Depositor), 0.156 (DCC)
R-Value Observed:
0.151 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

The crystal structure of the human RAC3 in complex with the CRIB domain of human p21-activated kinase 1 (PAK1).

Ugochukwu, E., Yang, X., Elkins, J.M., Burgess-Brown, N., Bunkoczi, G., Knapp, S., Doyle, D.

To be published.

Macromolecule Content

Total Structure Weight: 24.73 kDa
Atom Count: 1,863
Modeled Residue Count: 202
Deposited Residue Count: 215
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ras-related C3 botulinum toxin substrate 3	A	179	Homo sapiens	Mutation(s): 0 Gene Names: RAC3 EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for P60763 (Homo sapiens) Explore P60763 Go to UniProtKB: P60763
PHAROS: P60763 GTEx: ENSG00000169750
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P60763
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
CRIB domain of the Serine/threonine-protein kinase PAK 1	B [auth I]	36	N/A	Mutation(s): 0 EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q13153 (Homo sapiens) Explore Q13153 Go to UniProtKB: Q13153
PHAROS: Q13153 GTEx: ENSG00000149269
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q13153
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GCP Query on GCP Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER C₁₁ H₁₈ N₅ O₁₃ P₃ PHBDHXOBFUBCJD-KQYNXXCUSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A]	E [auth A], F [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free: 0.192 (Depositor), 0.200 (DCC)
R-Value Work: 0.149 (Depositor), 0.156 (DCC)
R-Value Observed: 0.151 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.226	α = 90
b = 53.48	β = 93.45
c = 47.682	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
CrystalClear	data collection
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2007-08-28

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2007-08-28
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2023-08-30
Changes: Data collection, Database references, Derived calculations, Refinement description