2OV2 | pdb_00002ov2

The crystal structure of the human RAC3 in complex with the CRIB domain of human p21-activated kinase 4 (PAK4)

PDB DOI: https://doi.org/10.2210/pdb2OV2/pdb

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

Deposited: 2007-02-12 Released: 2007-03-13
Deposition Author(s): Ugochukwu, E., Yang, X., Elkins, J.M., Burgess-Brown, N., Bunkoczi, G., Debreczeni, J.E.D., Sundstrom, M., Arrowsmith, C.H., Weigelt, J., Edwards, A., von Delft, F., Knapp, S., Doyle, D.A., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.225 (Depositor), 0.230 (DCC)
R-Value Work:
0.172 (Depositor), 0.180 (DCC)
R-Value Observed:
0.174 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 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 4 (PAK4)

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

To be published.

Macromolecule Content

Total Structure Weight: 197.57 kDa
Atom Count: 14,479
Modelled Residue Count: 1,699
Deposited Residue Count: 1,712
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ras-related C3 botulinum toxin substrate 3	A B [auth F] C [auth B] D [auth C] E [auth G] A, B [auth F], C [auth B], D [auth C], E [auth G], F [auth D], G [auth E], H	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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P60763
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein kinase PAK 4	I, J, K, L, M I, J, K, L, M, N, O, P	35	Homo sapiens	Mutation(s): 0 Gene Names: PAK4, KIAA1142 EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for O96013 (Homo sapiens) Explore O96013 Go to UniProtKB: O96013
PHAROS: O96013 GTEx: ENSG00000130669
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O96013
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GCP Query on GCP Download Ideal Coordinates CCD File SDF format, chain CA [auth C] SDF format, chain FA [auth G] SDF format, chain HA [auth D] SDF format, chain LA [auth E] SDF format, chain NA [auth H] SDF format, chain T [auth A] SDF format, chain V [auth F] SDF format, chain Z [auth B] MOL2 format, chain CA [auth C] MOL2 format, chain FA [auth G] MOL2 format, chain HA [auth D] MOL2 format, chain LA [auth E] MOL2 format, chain NA [auth H] MOL2 format, chain T [auth A] MOL2 format, chain V [auth F] MOL2 format, chain Z [auth B] mmCIF format, chain CA [auth C] mmCIF format, chain FA [auth G] mmCIF format, chain HA [auth D] mmCIF format, chain LA [auth E] mmCIF format, chain NA [auth H] mmCIF format, chain T [auth A] mmCIF format, chain V [auth F] mmCIF format, chain Z [auth B]	CA [auth C] FA [auth G] HA [auth D] LA [auth E] NA [auth H] CA [auth C], FA [auth G], HA [auth D], LA [auth E], NA [auth H], T [auth A], V [auth F], Z [auth B]	PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER C₁₁ H₁₈ N₅ O₁₃ P₃ PHBDHXOBFUBCJD-KQYNXXCUSA-N		Interactions Focus chain CA [auth C] Focus chain FA [auth G] Focus chain HA [auth D] Focus chain LA [auth E] Focus chain NA [auth H] Focus chain T [auth A] Focus chain V [auth F] Focus chain Z [auth B] Interactions & Density Focus chain CA [auth C] Focus chain FA [auth G] Focus chain HA [auth D] Focus chain LA [auth E] Focus chain NA [auth H] Focus chain T [auth A] Focus chain V [auth F] Focus chain Z [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain DA [auth C] SDF format, chain IA [auth D] SDF format, chain W [auth F] MOL2 format, chain DA [auth C] MOL2 format, chain IA [auth D] MOL2 format, chain W [auth F] mmCIF format, chain DA [auth C] mmCIF format, chain IA [auth D] mmCIF format, chain W [auth F]	DA [auth C], IA [auth D], W [auth F]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain DA [auth C] Focus chain IA [auth D] Focus chain W [auth F] Interactions & Density Focus chain DA [auth C] Focus chain IA [auth D] Focus chain W [auth F]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain BA [auth C] SDF format, chain KA [auth E] SDF format, chain OA [auth N] SDF format, chain PA [auth O] SDF format, chain QA [auth P] SDF format, chain R [auth A] SDF format, chain S [auth A] SDF format, chain Y [auth B] MOL2 format, chain BA [auth C] MOL2 format, chain KA [auth E] MOL2 format, chain OA [auth N] MOL2 format, chain PA [auth O] MOL2 format, chain QA [auth P] MOL2 format, chain R [auth A] MOL2 format, chain S [auth A] MOL2 format, chain Y [auth B] mmCIF format, chain BA [auth C] mmCIF format, chain KA [auth E] mmCIF format, chain OA [auth N] mmCIF format, chain PA [auth O] mmCIF format, chain QA [auth P] mmCIF format, chain R [auth A] mmCIF format, chain S [auth A] mmCIF format, chain Y [auth B]	BA [auth C] KA [auth E] OA [auth N] PA [auth O] QA [auth P] BA [auth C], KA [auth E], OA [auth N], PA [auth O], QA [auth P], R [auth A], S [auth A], Y [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain BA [auth C] Focus chain KA [auth E] Focus chain OA [auth N] Focus chain PA [auth O] Focus chain QA [auth P] Focus chain R [auth A] Focus chain S [auth A] Focus chain Y [auth B] Interactions & Density Focus chain BA [auth C] Focus chain KA [auth E] Focus chain OA [auth N] Focus chain PA [auth O] Focus chain QA [auth P] Focus chain R [auth A] Focus chain S [auth A] Focus chain Y [auth B]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain EA [auth G] SDF format, chain GA [auth D] SDF format, chain JA [auth E] SDF format, chain MA [auth H] SDF format, chain Q [auth A] SDF format, chain U [auth F] SDF format, chain X [auth B] MOL2 format, chain AA [auth C] MOL2 format, chain EA [auth G] MOL2 format, chain GA [auth D] MOL2 format, chain JA [auth E] MOL2 format, chain MA [auth H] MOL2 format, chain Q [auth A] MOL2 format, chain U [auth F] MOL2 format, chain X [auth B] mmCIF format, chain AA [auth C] mmCIF format, chain EA [auth G] mmCIF format, chain GA [auth D] mmCIF format, chain JA [auth E] mmCIF format, chain MA [auth H] mmCIF format, chain Q [auth A] mmCIF format, chain U [auth F] mmCIF format, chain X [auth B]	AA [auth C] EA [auth G] GA [auth D] JA [auth E] MA [auth H] AA [auth C], EA [auth G], GA [auth D], JA [auth E], MA [auth H], Q [auth A], U [auth F], X [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain EA [auth G] Focus chain GA [auth D] Focus chain JA [auth E] Focus chain MA [auth H] Focus chain Q [auth A] Focus chain U [auth F] Focus chain X [auth B] Interactions & Density Focus chain AA [auth C] Focus chain EA [auth G] Focus chain GA [auth D] Focus chain JA [auth E] Focus chain MA [auth H] Focus chain Q [auth A] Focus chain U [auth F] Focus chain X [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.225 (Depositor), 0.230 (DCC)
R-Value Work: 0.172 (Depositor), 0.180 (DCC)
R-Value Observed: 0.174 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.843	α = 88.58
b = 73.859	β = 87.76
c = 133.84	γ = 70.64

Software Package:

Software Name	Purpose
REFMAC	refinement
MAR345	data collection
MOSFLM	data reduction
CCP4	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2007-03-13

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2007-03-13
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.3: 2017-10-18
Changes: Refinement description
Version 1.4: 2023-08-30
Changes: Data collection, Database references, Derived calculations, Refinement description