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9r2c

CpKRS in complex with inhibitor DDD01038762

Method: X-RAY DIFFRACTION D_max: 105.5 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9r2c
deposition_date	2025-04-29
last_revision	2026-06-10
title	CpKRS in complex with inhibitor DDD01038762
keywords	inhibitor, LIGASE; LIGASE
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	32.56 Å
rg_electron	31.96 Å
i0	394303000.00
molecular_weight	107600.0 kDa
excluded_volume	104510 Å³
envelope_volume	178090 Å³
shell_volume	46139 Å³
envelope_diameter	116.4 Å
shell_rg	39.11 Å
envelope_rg	32.14 Å
shape_rg	31.92 Å
total_rg	32.43 Å
total_atoms	8139
n_residues	998
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	105.5 Å
rg_real	32.54 Å
rg_real_error	0.78 Å
i0_real	3.9430e+08
i0_real_error	5.9340e+06
rg_reciprocal	32.55 Å
i0_reciprocal	394300000.0000
total_estimate	0.8202
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	38.8 Å
skewness	0.340
kurtosis	-0.364
angular_range	— – 0.2450 Å⁻¹
current_alpha	0.0000
highest_alpha	60590000.0000
n_real_points	50
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.888; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	Lysine--tRNA ligase
formula_weight	61459.1 kDa
ec_number	6.1.1.6
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	8884

MAHHHHHHMGTLEAQTQGPGSHYTDNRYKMMECIKDAGRPFYPHKFKISMSLPAYALKYGNVENGYIDKDTTLSLSGRVTSIRSSSSKLIFYDIFCEEQKVQIIANIMEHDISTGEFSVSHSEIRRGDVVGFTGFPGKSKRGELSLFSKSVVLLSPCYHMLPTAISGLKDQEVRYRQRYLDLMLNEESRKVFKLRSRAIKYIRNYFDRLGFLEVETPMLNMIYGGAAARPFITYHNELETQLYMRIAPELYLKQLIVGGLDKVYEIGKNFRNEGIDLTHNPEFTAMEFYMAYADYYDLMDLTEELISGLVLEIHGSLKIPYHPDGPEGKCIEIDFTTPWKRFSFVEEIESGLGEKLKRPLDSQENIDFMVEMCEKHEIELPHPRTAAKLLDKLAGHFVETKCTNPSFIIDHPQTMSPLAKWHREKPEMTERFELFVLGKELCNAYTELNEPLQQRKFFEQQADAKASGDVEACPIDETFCLALEHGLPPTGGWGLGIDRLIMFLADKNNIKEVILFPAMRNVKQNAQHSNQHSGN

Source

organism	Cryptosporidium parvum Iowa II
ncbi_taxonomy_id	353152
host_organism	Escherichia coli

Entity 2 non-polymer

description	LYSINE
formula_weight	147.2 kDa
src_method	syn
entity_count	2

Entity 3 non-polymer

description	2-azanyl-6-cyclopentyl-7~{H}-pyrrolo[3,4-d]pyrimidin-5-one
formula_weight	218.3 kDa
src_method	syn
entity_count	2

Entity 4 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	nat
entity_count	1

Entity 5 non-polymer

description	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
formula_weight	122.1 kDa
src_method	syn
entity_count	1

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	739

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6. Citations (1)

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length_a	72.595 Å
length_b	116.129 Å
length_c	142.036 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 2 21 21
int_tables_number	18
crystal_system	—

resolution	1.840 Å
resolution_low	89.904 Å
r_factor	—
r_work	0.1622
r_free	0.1933

fit	/app/data/saxs_computation/r2/9r2c/9r2c.fit
pddf	/app/data/pr_computation/r2/9r2c/9r2c.pr.out
profile	/app/data/saxs_computation/r2/9r2c/9r2c.dat