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9z5w

Crystal structure of HRAS in complex with N-LHY affibody

Method: X-RAY DIFFRACTION D_max: 61.3 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9z5w
deposition_date	2025-11-12
last_revision	2026-06-03
title	Crystal structure of HRAS in complex with N-LHY affibody
keywords	Small GTPase, ONCOPROTEIN; ONCOPROTEIN
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	18.87 Å
rg_electron	17.93 Å
i0	10692800.00
molecular_weight	23564.0 kDa
excluded_volume	29185 Å³
envelope_volume	33909 Å³
shell_volume	16225 Å³
envelope_diameter	62.3 Å
shell_rg	23.63 Å
envelope_rg	18.40 Å
shape_rg	17.91 Å
total_rg	18.85 Å
total_atoms	3286
n_residues	206
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	61.3 Å
rg_real	18.84 Å
rg_real_error	0.45 Å
i0_real	1.0690e+07
i0_real_error	1.4000e+05
rg_reciprocal	18.84 Å
i0_reciprocal	10690000.0000
total_estimate	0.6430
solution_quality	REASONABLE a REASONABLE solution
n_peaks	2
r_peak_primary	22.1 Å
skewness	0.293
kurtosis	-0.362
angular_range	— – 0.4200 Å⁻¹
current_alpha	0.0000
highest_alpha	2348000.0000
n_real_points	73
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.880; Stabil: 0.998; Sysdev: 0.242; Positv: 1.000; Valcen: 0.993; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	GTPase HRas
formula_weight	19147.5 kDa
ec_number	3.6.5.2
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	3391

SNAMTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHQYREQIKRVKDSDDVPMVLVGNKCDLAARTVESRQAQDLARSYGIPYIETSAKTRQGVEDAFYTLVREIRQH

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 polymer

description	N-LHY affibody
formula_weight	6469.2 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

VDNKFNKELHYAIHEIGNLPNLNVYQIIAFVNSLDNDPSQSANLLAEAKKLNDAQAPK

Source

organism	unidentified
ncbi_taxonomy_id	32644
host_organism	Escherichia coli

Entity 3 non-polymer

description	GUANOSINE-5'-DIPHOSPHATE
formula_weight	443.2 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

description	1,2-ETHANEDIOL
formula_weight	62.1 kDa
src_method	syn
entity_count	1

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	87

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6. Citations (1)

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length_a	55.529 Å
length_b	55.529 Å
length_c	280.680 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	12

space_group	P 61 2 2
int_tables_number	178
crystal_system	monoclinic

resolution	1.800 Å
resolution_low	48.090 Å
r_factor	0.2038
r_work	0.2023
r_free	0.2238

fit	/app/data/saxs_computation/z5/9z5w/9z5w.fit
pddf	/app/data/pr_computation/z5/9z5w/9z5w.pr.out
profile	/app/data/saxs_computation/z5/9z5w/9z5w.dat

Crystal structure of HRAS in complex with N-LHY affibody

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 (5)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 non-polymer

Entity 4 non-polymer

Entity 5 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)