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9x7o

Lansoprazole derivative in complex with CRM1-Ran-RanBP1

Method: X-RAY DIFFRACTION D_max: 110.8 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9x7o
deposition_date	2025-10-17
title	Lansoprazole derivative in complex with CRM1-Ran-RanBP1
keywords	nuclear export inhibitor, TRANSPORT PROTEIN; TRANSPORT PROTEIN
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	36.27 Å
rg_electron	35.60 Å
i0	688044000.00
molecular_weight	143440.0 kDa
excluded_volume	139430 Å³
envelope_volume	257270 Å³
shell_volume	58082 Å³
envelope_diameter	123.1 Å
shell_rg	43.95 Å
envelope_rg	34.93 Å
shape_rg	35.59 Å
total_rg	36.01 Å
total_atoms	10856
n_residues	1330
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	110.8 Å
rg_real	36.01 Å
rg_real_error	0.50 Å
i0_real	6.8800e+08
i0_real_error	1.0530e+07
rg_reciprocal	36.17 Å
i0_reciprocal	688100000.0000
total_estimate	0.6821
solution_quality	REASONABLE a REASONABLE solution
n_peaks	2
r_peak_primary	47.8 Å
skewness	0.022
kurtosis	-0.607
angular_range	— – 0.2200 Å⁻¹
current_alpha	0.0001
highest_alpha	42660000.0000
n_real_points	45
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.939; Stabil: 1.000; Sysdev: 0.028; Positv: 1.000; Valcen: 0.981; Smooth: 0.982

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4. Crystallography & Experiment

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5. Entities & Polymer Info (11)

Entity 1 polymer

description	GTP-binding nuclear protein Ran
formula_weight	24399.1 kDa
ec_number	3.6.5.-
mutation	Q69L/L182A
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	12151

MAAQGEPQVQFKLVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGPIKFNVWDTAGLEKFGGLRDGYYIQAQCAIIMFDVTSRVTYKNVPNWHRDLVRVCENIPIVLCGNKVDIKDRKVKAKSIVFHRKKNLQYYDISAKSNYNFEKPFLWLARKLIGDPNLEFVAMPAAAPPEVVMDPALAAQYEHDLEVAQTTALPDEDDDL

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 polymer

description	Ran-specific GTPase-activating protein 1
formula_weight	16320.7 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

DIHFEPVVHLEKVDVKTMEEDEEVLYKVRAKLFRFDADAKEWKERGTGDCKFLKNKKTNKVRILMRRDKTLKICANHIIAPEYTLKPNVGSDRSWVYACTADIAEGEAEAFTFAIRFGSKENADKFKEEFEKAQEINKKA

Source

organism	Saccharomyces cerevisiae S288C
ncbi_taxonomy_id	559292
host_organism	Escherichia coli

Entity 3 polymer

description	Exportin-1
formula_weight	115224.5 kDa
mutation	S27E/Q49E/A51V/D537G/T539C/V540E/K541Q/S553R/Q561E/A741T/Y1022C
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	C

GGSMEGILDFSNDLDIALLDQVVSTFYQGEGVQQKQAQEILTKFQDNPDAWEKVDQILQFSTNPQSKFIALSILDKLITRKWKLLPNDHRIGIRNFVVGMIISMCQDDEVFKTQKNLINKSDLTLVQILKQEWPQNWPEFIPELIGSSSSSVNVCENNMIVLKLLSEEVFDFSAEQMTQAKALHLKNSMSKEFEQIFKLCFQVLEQGSSSSLIVATLESLLRYLHWIPYRYIYETNILELLSTKFMTSPDTRAITLKCLTEVSNLKIPQDNDLIKRQTVLFFQNTLQQIATSVMPVTADLKATYANANGNDQSFLQDLAMFLTTYLARNRALLESDESLRELLLNAHQYLIQLSKIEERELFKTTLDYWHNLVADLFYEPLKKHIYEEICSQLRLVIIENMVRPEEIQLYKSEREVLVYLTHLNVIDTEEIMISKLARQIDGSEWSWHNINTLSWAIGSISGTMSEDTEKRFVVTVIKDLLGLCEQKRGKDNKAVVARDIMYVVGEYPRFLKAHWNFLRTVILKLFEFMHETHEGVQDMACDTFIKIVQKCKYHFVIQQPRESEPFIQTIIRDIQKTTADLQPQQVHTFYKACGIIISEERSVAERNRLLSDLMQLPNMAWDTIVEQSTANPTLLLDSETVKIIANIIKTNVAVCTSMGADFYPQLGHIYYNMLQLYRAVSSMISTQVAAEGLIATKTPKVRGLRTIKKEILKLVETYISKARNLDDVVKVLVEPLLNAVLEDYMNNVPDARDAEVLNCMTTVVEKVGHMIPQGVILILQSVFECTLDMINKDFTEYPEHRVEFYKLLKVINEKSFAAFLELPPAAFKLFVDAICWAFKHNNRDVEVNGLQIALDLVKNIERMGNVPFANEFHKNYFFIFVSETFFVLTDSDHKSGFSKQALLLMKLISLVYDNKISVPLYQEAEVPQGTSNQVYLSQYLANMLSNAFPHLTSEQIASFLSALTKQCKDLVVFKGTLRDFLVQIKEVGGDPTDYLFAEDKENA

Source

organism	Saccharomyces cerevisiae S288C
ncbi_taxonomy_id	559292
host_organism	Escherichia coli

Entity 4 non-polymer

description	GUANOSINE-5'-TRIPHOSPHATE
formula_weight	523.2 kDa
src_method	nat
entity_count	1

Entity 5 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	nat
entity_count	3

Entity 6 non-polymer

description	3[N-MORPHOLINO]PROPANE SULFONIC ACID
formula_weight	209.3 kDa
src_method	syn
entity_count	1

Entity 7 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	5

Entity 8 non-polymer

description	DIMETHYL SULFOXIDE
formula_weight	78.1 kDa
src_method	syn
entity_count	3

Entity 9 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	3

Entity 10 non-polymer

description	[1-(1H-benzimidazol-2-yl)-3-methyl-4-[2,2,2-tris(fluoranyl)ethoxy]pyridin-1-ium-2-yl]methanethiol
formula_weight	354.4 kDa
src_method	syn
entity_count	1

Entity 11 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	1173

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6. Citations (1)

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length_a	105.888 Å
length_b	105.888 Å
length_c	305.588 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 43 21 2
int_tables_number	96
crystal_system	—

resolution	2.000 Å
resolution_low	32.350 Å
r_factor	0.1886
r_work	0.1870
r_free	0.2179

fit	/app/data/saxs_computation/x7/9x7o/9x7o.fit
pddf	/app/data/pr_computation/x7/9x7o/9x7o.pr.out
profile	/app/data/saxs_computation/x7/9x7o/9x7o.dat

Lansoprazole derivative in complex with CRM1-Ran-RanBP1

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

5. Entities & Polymer Info (11)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 non-polymer

Entity 7 non-polymer

Entity 8 non-polymer

Entity 9 non-polymer

Entity 10 non-polymer

Entity 11 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)