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9v6g

Human Pin1 (Peptidyl-prolyl cis-trans isomerase) catalytic domain in complex with a covalent inhibitor

Method: X-RAY DIFFRACTION D_max: 64.2 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9v6g
deposition_date	2025-05-27
last_revision	2026-06-10
title	Human Pin1 (Peptidyl-prolyl cis-trans isomerase) catalytic domain in complex with a covalent inhibitor
keywords	Human Pin1, Peptidyl-prolyl cis-trans isomerase, covalent inhibitor, ISOMERASE; ISOMERASE
method	X-RAY DIFFRACTION

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Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

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2. SAXS Parameters (CRYSOL)

rg_guinier	20.10 Å
rg_electron	19.43 Å
i0	24614000.00
molecular_weight	24527.0 kDa
excluded_volume	23179 Å³
envelope_volume	37761 Å³
shell_volume	16857 Å³
envelope_diameter	64.6 Å
shell_rg	24.74 Å
envelope_rg	19.46 Å
shape_rg	19.41 Å
total_rg	20.00 Å
total_atoms	1844
n_residues	226
n_harmonics	20
q_range	— – 0.5000 Å⁻¹
n_points	101
shell_type	directional
solvent_density	0.3340 e/Å³
contrast_shell	0.0300 e/Å³
crysol_version	4.1.3

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3. P(r) Analysis (GNOM)

dmax	64.2 Å
rg_real	20.10 Å
rg_real_error	0.38 Å
i0_real	2.4610e+07
i0_real_error	3.3070e+05
rg_reciprocal	20.10 Å
i0_reciprocal	24610000.0000
total_estimate	0.9050
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	22.0 Å
skewness	0.313
kurtosis	-0.483
angular_range	— – 0.3950 Å⁻¹
current_alpha	0.0000
highest_alpha	4221000.0000
n_real_points	71
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.931; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.983; Smooth: 0.983

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1
formula_weight	13402.9 kDa
ec_number	5.2.1.8
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	2092

GPGKNGQGEPARVRCSHLLVKHSQSRRPSSWRQEQITRTQEEALELINGYIQKIKSGEEDFESLASQFSDCSSAKARGDLGAFSRGQMQKPFEDASFALRTGEMSGPVFTDSGIHIILRTE

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	~{N}-(1-benzothiophen-2-ylmethyl)-~{N}-[(3~{R})-1,1-bis(oxidanylidene)thiolan-3-yl]-2-chloranyl-ethanamide
formula_weight	357.9 kDa
src_method	syn
entity_count	2

Entity 3 non-polymer

description	3-[bis(oxidanyl)methyl]pentane-1,1,3,5,5-pentol
formula_weight	198.2 kDa
src_method	nat
entity_count	2

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	248

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6. Citations (1)

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length_a	117.888 Å
length_b	36.377 Å
length_c	51.310 Å
angle_alpha	90.00 °
angle_beta	100.98 °
angle_gamma	90.00 °
z_pdb	8

space_group	C 1 2 1
int_tables_number	5
crystal_system	monoclinic

resolution	2.000 Å
resolution_low	34.850 Å
r_factor	0.2059
r_work	0.2053
r_free	0.2173

fit	/app/data/saxs_computation/v6/9v6g/9v6g.fit
pddf	/app/data/pr_computation/v6/9v6g/9v6g.pr.out
profile	/app/data/saxs_computation/v6/9v6g/9v6g.dat

Human Pin1 (Peptidyl-prolyl cis-trans isomerase) catalytic domain in complex with a covalent inhibitor

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

Unit Cell

Symmetry

Refinement

Diffraction