PDB-9jyr: Crystal structure of the PIN1 and fragment 4 complex

ID or keywords:

Entry

Database: PDB / ID: 9jyr

Title

Crystal structure of the PIN1 and fragment 4 complex

Components

Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1

Keywords

ISOMERASE / cis-trans isomerase

Function / homology

Function and homology information

cis-trans isomerase activity / phosphothreonine residue binding / negative regulation of cell motility / ubiquitin ligase activator activity / regulation of protein localization to nucleus / GTPase activating protein binding / mitogen-activated protein kinase kinase binding / protein targeting to mitochondrion / protein peptidyl-prolyl isomerization / regulation of mitotic nuclear division ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.65 Å

Authors

Xiao, Q.J. / Wu, T.T. / Shu, H.L. / Qin, W.M.

Funding support

1items

Citation

Journal: Eur.J.Med.Chem. / Year: 2025
Title: Uncovering druggable hotspots on Pin1 via X-ray crystallographic fragment screening.
Authors: Xiao, Q. / Tang, J. / Shu, H. / Wu, T. / Zhang, H. / Wang, W. / Wang, L. / Qin, W.

History

Deposition	Oct 12, 2024	Deposition site: PDBJ / Processing site: PDBC
Revision 1.0	Aug 27, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	9jyr.cif.gz	79.5 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	9jyr_validation.pdf.gz	1.3 MB	Display	wwPDB validaton report
Full document	9jyr_full_validation.pdf.gz	1.3 MB	Display
Data in XML	9jyr_validation.xml.gz	11.3 KB	Display
Data in CIF	9jyr_validation.cif.gz	15 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/jy/9jyr ftp://data.pdbj.org/pub/pdb/validation_reports/jy/9jyr	HTTPS FTP

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Related structure data

Related structure data	9jyoC 9jypC 9jytC 9jyvC 9jz2C 9jz3C 9jz4C 9jz6C 9jzgC 9jzsC 9jzuC 9jzvC 9ke7C 9ke9C 9kebC 9kecC 9kelC 9keqC 9kesC 9kewC 9keyC 9kezC 9kf0C 9kfcC 9kfhC 9kg9C 9kxhC 9kxiC 9kxjC 9kxlC 9kxmC 9kxnC 9kxqC 9v92C C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#245 - May 2020 Spliceosomes similarity (8) #31 - Jul 2002 p53 Tumor Suppressor similarity (1) #122 - Feb 2010 Enhanceosome similarity (1) #213 - Sep 2017 Sirtuins similarity (1) #221 - May 2018 Human Papillomavirus and Vaccines similarity (1) #234 - Jun 2019 MDM2 and Cancer similarity (1) #163 - Jul 2013 HIV Capsid similarity (1)

Deposited unit

A: Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1

hetero molecules

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

1

Idetical with deposited unit
defined by author
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	69.393, 69.393, 79.998
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	152
Space group name H-M	P3₁21

#1: Protein	Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 / Peptidyl-prolyl cis-trans isomerase Pin1 / PPIase Pin1 / Rotamase Pin1 Mass: 18185.193 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PIN1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q13526, peptidylprolyl isomerase
#2: Chemical	ChemComp-A1ED0 / 1H-indol-4-ylmethanol / Indole-4-methanol Mass: 147.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₉H₉NO / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-PE8 / 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL Mass: 370.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₆H₃₄O₉
#4: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO₄
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 135 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.06 Å³/Da / Density % sol: 59.77 %
Crystal grow	Temperature: 277 K / Method: evaporation Details: 2.6M AMMONIUM SULPHATE, 0.1M HEPES BUFFER PH7.5, 1% PEG 40

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site: NFPSS

/ Beamline: BL18U / Wavelength: 0.96 Å

Detector

Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 27, 2024

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.96 Å / Relative weight: 1

Reflection

Resolution: 1.65→50 Å / Num. obs: 27408 / % possible obs: 99.9 % / Redundancy: 19.7 % / CC_1/2: 0.999 / CC star: 1 / R_merge(I) obs: 0.157 / R_pim(I) all: 0.036 / R_rim(I) all: 0.161 / Χ²: 1.115 / Net I/σ(I): 4.5 / Num. measured all: 540195

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	CC star	R_pim(I) all	R_rim(I) all	Χ²	% possible all
1.65-1.68	20.2	3.429	1338	0.877	0.967	0.765	3.514	0.508	99.6
1.68-1.71	20.1	2.742	1361	0.909	0.976	0.616	2.811	0.517	99.6
1.71-1.74	19.5	2.315	1359	0.94	0.984	0.532	2.376	0.555	99.7
1.74-1.78	20.3	1.902	1328	0.939	0.984	0.425	1.949	0.547	100
1.78-1.82	20.2	1.324	1339	0.971	0.993	0.298	1.358	0.589	99.8
1.82-1.86	19.9	1.204	1367	0.967	0.992	0.273	1.235	0.618	99.9
1.86-1.9	20.7	2.616	1348	0.976	0.994	0.579	2.681	0.716	99.9
1.9-1.96	18.8	1.263	1346	0.958	0.989	0.299	1.299	2.281	99.9
1.96-2.01	20.3	0.687	1349	0.987	0.997	0.154	0.704	0.771	99.9
2.01-2.08	19.5	0.43	1372	0.989	0.997	0.099	0.441	0.854	100
2.08-2.15	20.4	0.353	1364	0.991	0.998	0.079	0.362	0.885	100
2.15-2.24	19	0.327	1365	0.994	0.999	0.077	0.336	1.044	100
2.24-2.34	18.2	0.303	1347	0.98	0.995	0.079	0.313	1.68	100
2.34-2.46	20.6	0.19	1392	0.996	0.999	0.043	0.194	1.058	100
2.46-2.62	19.8	0.154	1348	0.996	0.999	0.035	0.158	1.183	100
2.62-2.82	20.3	0.132	1386	0.997	0.999	0.03	0.136	1.31	100
2.82-3.11	20.1	0.106	1383	0.997	0.999	0.024	0.109	1.531	100
3.11-3.55	20.2	0.089	1407	0.998	1	0.02	0.092	1.885	100
3.55-4.48	18.5	0.085	1408	0.998	1	0.02	0.087	2.313	100
4.48-50	18	0.067	1501	0.998	0.999	0.016	0.069	1.59	99.9

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Processing

Software

Name	Version	Classification
PHENIX	(1.19_4092: ???)	refinement
HKL-3000		data scaling
HKL-3000		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.65→30.05 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.97 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2176	2001	7.37 %
R_work	0.2054	-	-
obs	0.2063	27152	99.11 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.65→30.05 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1211	0	10	135	1356

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	1245
X-RAY DIFFRACTION	f_angle_d	0.92	1664
X-RAY DIFFRACTION	f_dihedral_angle_d	8.57	206
X-RAY DIFFRACTION	f_chiral_restr	0.053	163
X-RAY DIFFRACTION	f_plane_restr	0.013	213

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.65-1.69	0.3511	142	0.3159	1780	X-RAY DIFFRACTION	99
1.69-1.74	0.3137	144	0.2815	1781	X-RAY DIFFRACTION	100
1.74-1.79	0.2814	139	0.2622	1774	X-RAY DIFFRACTION	100
1.79-1.84	0.2667	143	0.2164	1776	X-RAY DIFFRACTION	100
1.84-1.91	0.3008	138	0.2658	1730	X-RAY DIFFRACTION	97
1.91-1.99	0.313	137	0.2947	1698	X-RAY DIFFRACTION	94
1.99-2.08	0.2308	144	0.2027	1802	X-RAY DIFFRACTION	100
2.08-2.19	0.2069	141	0.2151	1797	X-RAY DIFFRACTION	100
2.19-2.32	0.218	144	0.2465	1792	X-RAY DIFFRACTION	98
2.32-2.5	0.2187	139	0.2002	1799	X-RAY DIFFRACTION	100
2.5-2.75	0.1997	145	0.2156	1809	X-RAY DIFFRACTION	100
2.75-3.15	0.2184	147	0.2002	1830	X-RAY DIFFRACTION	100
3.15-3.97	0.1966	143	0.1801	1843	X-RAY DIFFRACTION	100
3.97-30.05	0.1887	155	0.1742	1940	X-RAY DIFFRACTION	100

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	4.246	1.1999	-0.7352	4.4646	-0.5078	3.4919	-0.162	0.8169	-0.937	-0.4193	0.3955	-1.4807	0.5833	0.2774	-0.0823	0.4382	-0.083	-0.0234	0.3151	-0.0427	0.566	-14.8098	17.4627	1.8606
2	2.9883	1.8445	-0.7578	2.2038	0.59	2.0147	0.0641	-0.0176	-0.1702	0.0221	-0.1045	-0.4986	0.02	0.5038	0.0694	0.3234	-0.1399	0.0163	0.2857	0.0082	0.3048	-16.6181	21.8509	4.6679
3	3.2908	-2.2018	0.2192	2.947	-0.0465	2.5774	-0.1156	-0.2789	-0.3043	-0.1108	0.2563	0.3968	0.8952	-0.4179	-0.1196	0.2664	-0.1323	-0.0036	0.2528	0.0261	0.181	-31.6421	17.3249	18.2673
4	4.2033	0.6366	1.5317	2.6054	0.0398	0.57	0.0758	0.2174	-0.4538	-0.3138	-0.1285	0.1747	0.3181	-0.4445	-0.2871	0.0383	-0.2536	-0.1147	0.8892	-0.0176	0.2626	-45.6196	23.5992	9.1376
5	2.676	0.4824	-0.8058	1.4535	-0.1549	2.4597	-0.0104	-0.0903	0.2314	-0.0954	0.0348	0.0395	-0.1539	-0.3815	-0.0101	0.1493	-0.0441	0.0006	0.2594	0.0201	0.2164	-34.4474	31.1558	13.9627
6	1.7008	-1.3102	-0.5765	1.0295	0.8675	2.3658	-0.1409	-0.0623	-0.2224	0.068	-0.0135	0.1273	0.9292	-0.6999	0.0773	0.343	-0.2224	0.0248	0.4141	0.0208	0.2679	-35.358	16.1244	19.2639
7	2.3511	-0.3562	0.3749	1.6166	-0.0336	1.9121	-0.0417	0.037	-0.0877	-0.1949	0.0963	-0.0702	0.6663	-0.2725	-0.0688	0.3041	-0.1575	0.0138	0.2304	-0.0025	0.1979	-28.6221	17.0057	12.1683

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 6 through 15 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 16 through 53 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 54 through 62 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 63 through 72 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 73 through 110 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 111 through 131 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 132 through 163 )

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