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9uvl

Crystal structure of AGAP1-GDP complex

Method: X-RAY DIFFRACTION D_max: 130.9 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9uvl
deposition_date	2025-05-10
title	Crystal structure of AGAP1-GDP complex
keywords	Triple-negative breast cancer; AGAP1; noncanonical GDP binding; carcinogenesis, structure biology, CELL INVASION; CELL INVASION
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	41.18 Å
rg_electron	40.67 Å
i0	359806000.00
molecular_weight	151590.0 kDa
excluded_volume	188310 Å³
envelope_volume	263530 Å³
shell_volume	54808 Å³
envelope_diameter	129.6 Å
shell_rg	45.88 Å
envelope_rg	39.26 Å
shape_rg	40.67 Å
total_rg	40.95 Å
total_atoms	21002
n_residues	1315
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	130.9 Å
rg_real	41.02 Å
rg_real_error	0.96 Å
i0_real	3.5980e+08
i0_real_error	6.0430e+06
rg_reciprocal	41.18 Å
i0_reciprocal	359900000.0000
total_estimate	0.8945
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	55.1 Å
skewness	0.091
kurtosis	-0.527
angular_range	— – 0.1900 Å⁻¹
current_alpha	0.0000
highest_alpha	27140000.0000
n_real_points	39
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.899; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.932

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Arf-GAP with GTPase, ANK repeat and PH domain-containing protein 1
formula_weight	19354.9 kDa
src_method	man
entity_count	8

Polymer

type	polypeptide(L)
strand_id	A,B,C,D,E,F,G,H
atom_count	21066

GSHMLEPELKVGIVGNLASGKSALVHRYLTGTYVQEESPEGGRFKKEIVVDGQSYLLLIRDEGGPPEAQFAMWVDAVIFVFSLEDEISFQTVYHYYSRMANYRNTSEIPLVLVGTQDAISSANPRVIDDARARKLSNDLKRCTYYETCATYGLNVERVFQDVAQKIVATRKK

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia phage EcSzw_1

Entity 2 non-polymer

description	GUANOSINE-5'-DIPHOSPHATE
formula_weight	443.2 kDa
src_method	syn
entity_count	8

Entity 3 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	21

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	64

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6. Citations (1)

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length_a	114.405 Å
length_b	124.678 Å
length_c	127.604 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	32

space_group	P 21 21 21
int_tables_number	19
crystal_system	—

resolution	2.490 Å
resolution_low	35.170 Å
r_factor	0.2210
r_work	0.2190
r_free	0.2680

fit	/app/data/saxs_computation/uv/9uvl/9uvl.fit
pddf	/app/data/pr_computation/uv/9uvl/9uvl.pr.out
profile	/app/data/saxs_computation/uv/9uvl/9uvl.dat

Crystal structure of AGAP1-GDP complex

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