PDB-9jyv: Crystal structure of the PIN1 and fragment 6 complex.

ID or keywords:

Entry

Database: PDB / ID: 9jyv

Title

Crystal structure of the PIN1 and fragment 6 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: 1.8 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	9jyv.cif.gz	79.5 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	9jyv_validation.pdf.gz	1.3 MB	Display	wwPDB validaton report
Full document	9jyv_full_validation.pdf.gz	1.3 MB	Display
Data in XML	9jyv_validation.xml.gz	10.6 KB	Display
Data in CIF	9jyv_validation.cif.gz	14 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/jy/9jyv ftp://data.pdbj.org/pub/pdb/validation_reports/jy/9jyv	HTTPS FTP

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Related structure data

Related structure data	9jyoC 9jypC 9jyrC 9jytC 9jz2C 9jz3C 9jz4C 9jz6C 9jzgC 9jzsC 9jzuC 9jzvC 9ke7C 9ke9C 9kebC 9kecC 9kelC 9keqC 9kesC 9kewC 9keyC 9kezC 9kf0C 9kfcC 9kfhC 9kg9C 9kx7C 9kx9C 9kxcC 9kxdC 9kxeC 9kxfC 9kxgC 9kxhC 9kxiC 9kxjC 9kxlC 9kxmC 9kxnC 9kxoC 9kxpC 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)	69.442, 69.442, 79.471
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	152
Space group name H-M	P3₁21

Components on special symmetry positions

ID	Model	Components
1	1	A-203- A1ED2
2	1	A-203- A1ED2
3	1	A-203- A1ED2

#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-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
#3: Chemical	ChemComp-A1ED2 / 1-methylpyridin-2-one / 694-85-9 Mass: 109.126 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₆H₇NO / Feature type: SUBJECT OF INVESTIGATION
#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.: 116 / 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: 3.04 Å³/Da / Density % sol: 59.56 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion Details: 2.6M AMMONIUM SULPHATE, 0.1M HEPES BUFFER PH7.5, 1% PEG 400

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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: 1.8→50 Å / Num. obs: 20993 / % possible obs: 100 % / Redundancy: 18.2 % / CC_1/2: 0.992 / CC star: 0.998 / R_merge(I) obs: 0.187 / R_pim(I) all: 0.044 / R_rim(I) all: 0.193 / Χ²: 1.042 / Net I/σ(I): 3.2 / Num. measured all: 381097

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
1.8-1.83	12.6	2.783	1031	0.905	0.975	0.806	2.9	0.453	100
1.83-1.86	15.2	1.251	1017	0.957	0.989	0.326	1.294	0.472	100
1.86-1.9	16.1	1.805	1045	0.962	0.99	0.46	1.863	0.501	100
1.9-1.94	16.6	1.315	1033	0.929	0.981	0.332	1.357	1.22	100
1.94-1.98	17	1.029	1027	0.969	0.992	0.254	1.061	0.52	100
1.98-2.03	17	0.73	1046	0.976	0.994	0.179	0.752	0.549	100
2.03-2.08	16.5	0.658	1028	0.981	0.995	0.164	0.679	0.58	100
2.08-2.13	18.1	0.572	1027	0.987	0.997	0.137	0.588	0.602	100
2.13-2.2	18.3	0.505	1048	0.99	0.997	0.12	0.519	0.634	100
2.2-2.27	18.4	0.832	1030	0.975	0.994	0.198	0.855	1.809	100
2.27-2.35	20.4	0.675	1047	0.99	0.997	0.153	0.692	0.755	100
2.35-2.44	20.4	0.393	1044	0.997	0.999	0.089	0.403	0.726	100
2.44-2.55	20.1	0.317	1052	0.994	0.998	0.072	0.325	0.81	100
2.55-2.69	19.6	0.272	1036	0.994	0.998	0.063	0.279	0.9	100
2.69-2.86	20.1	0.23	1058	0.995	0.999	0.052	0.236	1.046	100
2.86-3.08	20	0.176	1062	0.995	0.999	0.04	0.181	1.266	100
3.08-3.39	20.3	0.148	1050	0.996	0.999	0.034	0.152	1.623	100
3.39-3.88	19.2	0.125	1072	0.996	0.999	0.029	0.129	2.057	100
3.88-4.88	19.3	0.099	1080	0.998	0.999	0.023	0.101	1.951	100
4.88-50	17.5	0.091	1160	0.998	0.999	0.022	0.094	1.675	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: 1.8→28.12 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 31.16 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2398	1979	9.52 %	1
R_work	0.214	-	-	-
obs	0.2164	20779	99.15 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.8→28.12 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1180	0	35	116	1331

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	1237
X-RAY DIFFRACTION	f_angle_d	0.938	1652
X-RAY DIFFRACTION	f_dihedral_angle_d	8.302	196
X-RAY DIFFRACTION	f_chiral_restr	0.055	163
X-RAY DIFFRACTION	f_plane_restr	0.012	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 (%)
1.8-1.85	0.3772	139	0.3181	1319	X-RAY DIFFRACTION	99
1.85-1.9	0.358	138	0.3084	1309	X-RAY DIFFRACTION	99
1.9-1.95	0.505	140	0.4472	1308	X-RAY DIFFRACTION	98
1.95-2.02	0.3122	135	0.257	1301	X-RAY DIFFRACTION	100
2.02-2.09	0.2813	144	0.2385	1353	X-RAY DIFFRACTION	99
2.09-2.17	0.2563	139	0.216	1329	X-RAY DIFFRACTION	100
2.17-2.27	0.334	133	0.3147	1291	X-RAY DIFFRACTION	97
2.27-2.39	0.3112	141	0.2425	1356	X-RAY DIFFRACTION	99
2.39-2.54	0.2257	138	0.2275	1320	X-RAY DIFFRACTION	99
2.54-2.73	0.2458	146	0.2113	1358	X-RAY DIFFRACTION	100
2.74-3.01	0.218	145	0.216	1368	X-RAY DIFFRACTION	100
3.01-3.44	0.216	142	0.2039	1351	X-RAY DIFFRACTION	100
3.44-4.33	0.1974	147	0.1677	1389	X-RAY DIFFRACTION	100
4.34-28.12	0.2051	152	0.1833	1448	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	3.9395	-0.7729	-0.2049	4.4325	0.5571	4.1735	-0.1072	0.5562	0.2853	-0.1651	0.1304	0.8001	-0.7124	-0.4345	0.0878	0.6118	-0.083	-0.0026	0.4053	0.0426	0.5145	15.0302	-17.4182	1.7218
2	3.5355	1.9744	0.3018	1.7747	-0.5112	2.5526	0.0929	0.2272	0.1672	0.0628	-0.0567	0.2913	-0.1647	-0.484	-0.0028	0.4726	-0.1321	-0.0171	0.4253	0.0181	0.3585	16.6412	-21.7074	4.6626
3	3.293	-1.3304	-0.1085	2.6022	-0.6634	2.7407	0.009	-0.2058	0.3502	0.0184	0.1068	-0.3986	-0.9636	0.3463	-0.104	0.4241	-0.1591	0.0069	0.4141	-0.0395	0.2803	31.8257	-17.3121	18.0419
4	3.2929	-0.3532	-1.4729	4.9922	-0.1878	2.1818	-0.1306	0.4137	0.1471	-0.7072	0.2326	-0.3071	-0.6979	0.5561	-0.1529	0.3565	-0.2638	0.0554	0.9025	-0.0728	0.4272	45.6569	-23.6722	9.0925
5	3.8232	0.0787	0.6772	1.3824	0.597	1.9324	-0.0246	-0.3427	-0.4025	-0.0881	0.1399	-0.1312	0.0631	0.4723	-0.1439	0.2479	-0.0711	0.0111	0.4131	-0.0301	0.2789	34.3887	-31.2311	13.8555
6	2.6085	-1.0103	-1.1069	3.1545	-1.0576	1.4704	-0.2543	-0.3276	0.1467	0.0317	0.1513	0.1142	-0.7563	0.9848	0.1982	0.4918	-0.2555	-0.0422	0.577	-0.0615	0.29	35.5704	-16.2898	18.9776
7	2.8786	0.7267	-0.8383	2.2154	-0.4598	2.9799	-0.0258	0.0661	0.2184	-0.3189	0.1342	-0.063	-0.9527	0.4068	-0.037	0.4154	-0.1769	-0.0232	0.3376	-0.0094	0.2079	28.7051	-16.9421	12.0885

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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