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9upd

Crystal structure of human serum albumin complex with nateglinide

Method: X-RAY DIFFRACTION D_max: 114.5 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9upd
deposition_date	2025-04-28
title	Crystal structure of human serum albumin complex with nateglinide
keywords	Human serum albumin, nateglinide, complex, 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	35.82 Å
rg_electron	35.39 Å
i0	446387000.00
molecular_weight	112490.0 kDa
excluded_volume	108060 Å³
envelope_volume	205240 Å³
shell_volume	48962 Å³
envelope_diameter	124.0 Å
shell_rg	41.63 Å
envelope_rg	34.27 Å
shape_rg	35.36 Å
total_rg	35.78 Å
total_atoms	8457
n_residues	1118
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	114.5 Å
rg_real	35.75 Å
rg_real_error	0.83 Å
i0_real	4.4640e+08
i0_real_error	6.2550e+06
rg_reciprocal	35.80 Å
i0_reciprocal	446400000.0000
total_estimate	0.8954
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	44.2 Å
skewness	0.262
kurtosis	-0.393
angular_range	— – 0.2200 Å⁻¹
current_alpha	0.0000
highest_alpha	25470000.0000
n_real_points	45
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.929; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.848

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	Serum albumin
formula_weight	66571.2 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	8471

DAHKSEVAHRFKDLGEENFKALVLIAFAQYLQQCPFEDHVKLVNEVTEFAKTCVADESAENCDKSLHTLFGDKLCTVATLRETYGEMADCCAKQEPERNECFLQHKDDNPNLPRLVRPEVDVMCTAFHDNEETFLKKYLYEIARRHPYFYAPELLFFAKRYKAAFTECCQAADKAACLLPKLDELRDEGKASSAKQRLKCASLQKFGERAFKAWAVARLSQRFPKAEFAEVSKLVTDLTKVHTECCHGDLLECADDRADLAKYICENQDSISSKLKECCEKPLLEKSHCIAEVENDEMPADLPSLAADFVESKDVCKNYAEAKDVFLGMFLYEYARRHPDYSVVLLLRLAKTYETTLEKCCAAADPHECYAKVFDEFKPLVEEPQNLIKQNCELFEQLGEYKFQNALLVRYTKKVPQVSTPTLVEVSRNLGKVGSKCCKHPEAKRMPCAEDYLSVVLNQLCVLHEKTPVSDRVTKCCTESLVNRRPCFSALEVDETYVPKEFNAETFTFHADICTLSEKERQIKKQTALVELVKHKPKATKEQLKAVMDDFAAFVEKCCKADDKETCFAEEGKKLVAASQAALGL

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Komagataella pastoris

Entity 2 non-polymer

description	(2R)-3-phenyl-2-[(4-propan-2-ylcyclohexyl)carbonylamino]propanoic acid
formula_weight	317.4 kDa
src_method	nat
entity_count	2

Entity 3 non-polymer

description	PHOSPHATE ION
formula_weight	95.0 kDa
src_method	syn
entity_count	2

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6. Citations (1)

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length_a	59.450 Å
length_b	180.800 Å
length_c	60.290 Å
angle_alpha	90.00 °
angle_beta	105.64 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 1 21 1
int_tables_number	4
crystal_system	monoclinic

resolution	2.800 Å
resolution_low	47.700 Å
r_factor	0.2494
r_work	0.2474
r_free	0.2874

fit	/app/data/saxs_computation/up/9upd/9upd.fit
pddf	/app/data/pr_computation/up/9upd/9upd.pr.out
profile	/app/data/saxs_computation/up/9upd/9upd.dat

Crystal structure of human serum albumin complex with nateglinide

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