PDB-2f57: Crystal Structure Of The Human P21-Activated Kinase 5

ID or keywords:

Entry

Database: PDB / ID: 2f57

Title

Crystal Structure Of The Human P21-Activated Kinase 5

Components

Serine/threonine-protein kinase PAK 7

Keywords

TRANSFERASE / Pak5 / Kinase domains / GroupII PAKs / Structural Genomics / Structural Genomics Consortium / SGC

Function / homology

Function and homology information

RHOD GTPase cycle / Activation of RAC1 / regulation of MAPK cascade / CDC42 GTPase cycle / RHOH GTPase cycle / cytoskeleton organization / RAC1 GTPase cycle / learning / negative regulation of extrinsic apoptotic signaling pathway / locomotory behavior ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.8 Å

Authors

Eswaran, J. / Turnbull, A. / Ugochukwu, E. / Papagrigoriou, E. / Bray, J. / Das, S. / Savitsky, P. / Smee, C. / Burgess, N. / Fedorov, O. ...

Citation

Journal: Structure / Year: 2007
Title: Crystal Structures of the p21-activated kinases PAK4, PAK5, and PAK6 reveal catalytic domain plasticity of active group II PAKs.
Authors: Eswaran, J. / Lee, W.H. / Debreczeni, J.E. / Filippakopoulos, P. / Turnbull, A. / Fedorov, O. / Deacon, S.W. / Peterson, J.R. / Knapp, S.

History

Deposition	Nov 25, 2005	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 13, 2005	Provider: repository / Type: Initial release
Revision 1.1	May 1, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.3	Jan 31, 2018	Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4	Aug 23, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	2f57.cif.gz	148.9 KB	Display	PDBx/mmCIF format
PDB format	pdb2f57.ent.gz	114.3 KB	Display	PDB format
PDBx/mmJSON format	2f57.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	2f57_validation.pdf.gz	829.5 KB	Display	wwPDB validaton report
Full document	2f57_full_validation.pdf.gz	832.3 KB	Display
Data in XML	2f57_validation.xml.gz	30 KB	Display
Data in CIF	2f57_validation.cif.gz	45.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/f5/2f57 ftp://data.pdbj.org/pub/pdb/validation_reports/f5/2f57	HTTPS FTP

-
Related structure data

Related structure data	2bvaC 2c30SC 2cdzC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	2orp-d 2orr-d 4krm-6 2ors-d 1dd7-d 5mgy-8 5o7i-d 5bw0-3 6oag-d 5jv2-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#245 - May 2020 Spliceosomes similarity (2) #35 - Nov 2002 Ferritin and Transferrin similarity (3) #148 - Apr 2012 Ras Protein similarity (2) #214 - Oct 2017 Chimeric Antigen Receptors similarity (1)

Deposited unit

A: Serine/threonine-protein kinase PAK 7

B: Serine/threonine-protein kinase PAK 7

hetero molecules

73.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Serine/threonine-protein kinase PAK 7

hetero molecules

defined by author
36.5 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Serine/threonine-protein kinase PAK 7

hetero molecules

defined by author
36.6 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	98.661, 56.599, 120.764
Angle α, β, γ (deg.)	90.00, 103.13, 90.00
Int Tables number	5
Space group name H-M	C121

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / End auth comp-ID: GLN / End label comp-ID: GLN / Refine code: 6

Dom-ID	Beg auth comp-ID	Beg label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	ASN	ASN	A	A	-6 - 715	16 - 313
2	LEU	LEU	B	B	-5 - 715	17 - 313

#1: Protein	Serine/threonine-protein kinase PAK 7 / p21-activated kinase 7 / PAK-7 / PAK-5 Mass: 36248.730 Da / Num. of mol.: 2 / Fragment: residues 425-719 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pLIC-SGC1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q9P286, EC: 2.7.1.37
#2: Chemical	ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₄H₁₂NO₃ / Comment: pH buffer*YM
#3: Chemical	ChemComp-23D / N2-[(1R,2S)-2-AMINOCYCLOHEXYL]-N6-(3-CHLOROPHENYL)-9-ETHYL-9H-PURINE-2,6-DIAMINE Mass: 385.894 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₉H₂₄ClN₇
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 613 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

Crystal	Density Matthews: 2.26 Å³/Da / Density % sol: 45.66 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 0.2M Na/KPO4, 0.1M BTProp 7.5, 20% PEG3350, 10% Ethelene glycol, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9788 Å
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 22, 2005
Radiation	Monochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9788 Å / Relative weight: 1
Reflection	Resolution: 1.8→50 Å / Num. obs: 60040 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shell	Resolution: 1.8→1.86 Å / % possible all: 94

-
Processing

Software

Name	Version	Classification
REFMAC	5.2.0019	refinement
HKL-2000		data reduction
SCALEPACK		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ID 2C30

2c30

Resolution: 1.8→50 Å / Cor.coef. F_o:F_c: 0.968 / Cor.coef. F_o:F_c free: 0.958 / SU B: 4.161 / SU ML: 0.068 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.11 / ESU R Free: 0.104 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.18513	3031	5 %	RANDOM
R_work	0.15363	-	-	-
all	0.15525	56997	-	-
obs	0.15525	56997	99.39 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 15.528 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.43 Å²	0 Å²	-0.8 Å²
2-	-	0.99 Å²	0 Å²
3-	-	-	-0.92 Å²

Refinement step

Cycle: LAST / Resolution: 1.8→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4687	0	43	613	5343

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.022	4883
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	3353
X-RAY DIFFRACTION	r_angle_refined_deg	1.226	1.985	6639
X-RAY DIFFRACTION	r_angle_other_deg	0.88	3.001	8143
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.257	5	614
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.933	23.16	212
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.337	15.036	845
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.633	15	42
X-RAY DIFFRACTION	r_chiral_restr	0.073	0.2	749
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	5379
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	977
X-RAY DIFFRACTION	r_nbd_refined	0.204	0.2	978
X-RAY DIFFRACTION	r_nbd_other	0.191	0.2	3655
X-RAY DIFFRACTION	r_nbtor_refined	0.171	0.2	2443
X-RAY DIFFRACTION	r_nbtor_other	0.083	0.2	2463
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.151	0.2	438
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.129	0.2	19
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.265	0.2	104
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.191	0.2	31
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	2.488	3	3101
X-RAY DIFFRACTION	r_mcbond_other	0.755	3	1205
X-RAY DIFFRACTION	r_mcangle_it	3.31	5	4902
X-RAY DIFFRACTION	r_scbond_it	5.206	7	2003
X-RAY DIFFRACTION	r_scangle_it	6.836	11	1728
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 3809 / Refine-ID: X-RAY DIFFRACTION

Type	Rms dev position (Å)	Weight position
loose positional	1.39	5
loose thermal	2.48	10

LS refinement shell

Resolution: 1.8→1.847 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.236	201	-
R_work	0.182	3880	-
obs	-	-	92.02 %

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	0.4276	1.1072	-1.3016	3.4374	-3.0033	4.1965	0.1322	-0.0064	-0.1383	0.0416	0.0605	0.0054	0.0448	-0.2763	-0.1928	0.1788	0.0152	0.0228	0.4514	0.0598	0.1143	25.7178	19.039	50.5421
2	5.2914	0.9813	0.1215	3.8145	-1.1171	4.9262	-0.0595	-0.0811	-0.134	-0.1965	0.0204	0.3106	-0.0215	-0.1149	0.0391	0.2114	0.0976	-0.0442	0.3922	0.0235	0.1731	21.9373	18.6728	49.9759
3	4.504	-2.4848	1.718	5.0044	0.1872	3.581	-0.1761	-0.2251	0.258	0.0355	-0.0675	-0.0307	-0.0427	0.1191	0.2436	0.0879	0.0008	-0.0119	0.0508	-0.0107	0.0866	13.313	27.6278	32.1276
4	4.0767	-1.3662	2.0867	4.1148	-0.9936	4.5504	0.2315	0.0094	0.0319	-0.0973	-0.3004	0.0351	-0.0736	0.1937	0.0689	0.1411	0.058	-0.0216	0.3544	0.0021	0.09	30.1243	20.9191	51.0134
5	5.8504	-1.7541	-0.3304	5.418	-0.2434	8.1141	-0.0488	-0.159	0.302	-0.0212	0.1159	-0.2312	0.1811	0.0227	-0.067	0.1755	0.0136	-0.0501	0.1447	-0.0332	0.0638	10.9285	35.0082	38.8557
6	2.3017	-0.9104	0.1095	1.7088	0.306	1.5177	-0.0021	-0.0338	0.0799	-0.006	-0.0035	-0.006	0.0167	0.04	0.0056	0.0637	0.004	-0.0117	0.0662	0.005	0.0497	7.0847	29.4113	30.557
7	4.4889	-2.464	-0.6185	6.0486	2.1109	8.3651	0.1448	0.0129	0.1133	-0.1945	0.0032	-0.2368	-0.2589	-0.091	-0.148	0.0435	-0.0006	-0.0166	0.0627	0.0141	0.0981	-4.6305	35.5797	25.9114
8	2.2011	-0.0586	-0.233	1.9744	0.2771	2.0982	-0.0278	0.0415	0.0028	-0.0166	0.063	0.0069	0.0257	0.0171	-0.0352	0.036	0.012	-0.0067	0.0783	0.0117	0.0681	4.3825	29.2585	27.1776
9	1.7955	-1.4195	-1.046	2.7697	1.0578	1.8884	0.1277	-0.0491	0.0998	0.0756	-0.0143	0.0778	-0.23	-0.1274	-0.1134	0.0554	-0.0452	0.0502	0.0904	0.0047	0.0816	-5.0596	20.044	16.2584
10	1.4996	-1.0415	-0.4412	4.3611	2.2528	2.462	-0.0035	0.1098	-0.0608	0.0209	0.1028	-0.0844	0.0681	-0.0213	-0.0993	0.0913	-0.0157	-0.0042	0.0936	-0.0393	0.093	10.4506	17.5797	7.3498
11	0.6716	0.2633	1.6735	1.6896	2.8653	7.2465	-0.0839	0.0392	-0.0485	0.092	0.0431	-0.044	-0.018	-0.0269	0.0408	0.0194	-0.018	0.0057	0.0201	0.003	0.0575	16.5695	17.6886	21.2003
12	1.0692	0.2699	0.1521	0.3805	0.1416	0.3395	0.0387	-0.0066	-0.0018	0.0184	-0.0328	0.0063	0.0216	-0.0039	-0.0059	0.0105	-0.0018	0.0198	0.0175	-0.0037	0.0405	25.3562	22.3748	19.5527
13	1.7459	-0.1266	-0.1422	1.6493	0.0133	0.7374	0.037	-0.0012	0.0527	0.016	-0.0329	0.036	-0.0011	-0.0095	-0.004	-0.0046	-0.0006	0.0095	0.0277	-0.0009	0.0308	24.7229	23.1395	15.3966
14	1.2173	0.0002	-0.1342	2.363	-1.0938	2.0237	0.0252	0.038	0.014	0.0281	-0.0305	0.0002	0.0141	0.0557	0.0053	-0.0335	0.008	0.006	0.0291	0.0122	0.0352	34.4747	23.6552	13.0828
15	7.0291	5.0128	1.5489	9.0161	2.2053	6.016	0.2024	-0.3455	0.0259	0.1638	-0.2644	0.1071	0.0171	0.2325	0.062	0.0326	0.0451	0.0238	0.175	0.0781	0.1219	45.4955	21.787	13.0688
16	0.9291	0.1727	-0.254	1.1936	-0.0809	0.8961	0.0296	-0.0344	0.0208	0.0501	-0.0477	-0.0429	-0.0265	0.0639	0.0181	0.003	-0.0105	-0.0009	0.0621	-0.0021	0.0547	38.6973	26.8175	19.4546

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	X-RAY DIFFRACTION	1	A	A	-6 - 447	16 - 45
2	X-RAY DIFFRACTION	2	A	A	448 - 497	46 - 95
3	X-RAY DIFFRACTION	3	A	A	498 - 509	96 - 107
4	X-RAY DIFFRACTION	4	A	A	510 - 526	108 - 124
5	X-RAY DIFFRACTION	5	A	A	527 - 539	125 - 137
6	X-RAY DIFFRACTION	6	A	A	540 - 661	138 - 259
7	X-RAY DIFFRACTION	7	A	A	662 - 672	260 - 270
8	X-RAY DIFFRACTION	8	A	A	673 - 715	271 - 313
9	X-RAY DIFFRACTION	9	B	B	-5 - 441	17 - 39
10	X-RAY DIFFRACTION	10	B	B	442 - 481	40 - 79
11	X-RAY DIFFRACTION	11	B	B	482 - 501	80 - 99
12	X-RAY DIFFRACTION	12	B	B	502 - 561	100 - 159
13	X-RAY DIFFRACTION	13	B	B	562 - 594	160 - 192
14	X-RAY DIFFRACTION	14	B	B	595 - 652	193 - 250
15	X-RAY DIFFRACTION	15	B	B	653 - 662	251 - 260
16	X-RAY DIFFRACTION	16	B	B	663 - 718	261 - 316

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi