← Back to search

9v6p

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

Method: X-RAY DIFFRACTION D_max: 66.8 Å Quality: GOOD

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	9v6p
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

▼

Download Data

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

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	20.17 Å
rg_electron	19.47 Å
i0	24767800.00
molecular_weight	24562.0 kDa
excluded_volume	23189 Å³
envelope_volume	38190 Å³
shell_volume	16974 Å³
envelope_diameter	64.5 Å
shell_rg	24.96 Å
envelope_rg	19.53 Å
shape_rg	19.45 Å
total_rg	20.07 Å
total_atoms	1846
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

▼

3. P(r) Analysis (GNOM)

dmax	66.8 Å
rg_real	20.17 Å
rg_real_error	0.52 Å
i0_real	2.4770e+07
i0_real_error	3.5740e+05
rg_reciprocal	20.17 Å
i0_reciprocal	24770000.0000
total_estimate	0.8935
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	21.9 Å
skewness	0.314
kurtosis	-0.485
angular_range	— – 0.3950 Å⁻¹
current_alpha	0.0000
highest_alpha	4511000.0000
n_real_points	71
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.886; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.969; Smooth: 0.989

▶

4. Crystallography & Experiment

▶

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	2058

GPGKNGQGEPARVRCSHLLVKHSQSRRPSSWRQEQITRTQEEALELINGYIQKIKSGEEDFESLASQFSDCSSAKARGDLGAFSRGQMQKPFEDASFALRTGEMSGPVFTDSGIHIILRTE

Source

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

Entity 2 non-polymer

description	~{N}-[(3~{R})-1,1-bis(oxidanylidene)thiolan-3-yl]-2-chloranyl-~{N}-[(6-chloranyl-1~{H}-indol-3-yl)methyl]ethanamide
formula_weight	375.3 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	212

▶

6. Citations (1)

▶

length_a	117.874 Å
length_b	36.381 Å
length_c	51.309 Å
angle_alpha	90.00 °
angle_beta	100.75 °
angle_gamma	90.00 °
z_pdb	8

space_group	C 1 2 1
int_tables_number	5
crystal_system	monoclinic

resolution	1.990 Å
resolution_low	34.930 Å
r_factor	0.2124
r_work	0.2117
r_free	0.2260

fit	/app/data/saxs_computation/v6/9v6p/9v6p.fit
pddf	/app/data/pr_computation/v6/9v6p/9v6p.pr.out
profile	/app/data/saxs_computation/v6/9v6p/9v6p.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