← Back to search

9udm

Cocrystal structure of human cytosolic phenylalanyl-tRNA synthetase and an inhibitor in the presence of ATP

Method: X-RAY DIFFRACTION D_max: 120.3 Å Quality: GOOD

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	9udm
deposition_date	2025-04-07
last_revision	2026-04-15
title	Cocrystal structure of human cytosolic phenylalanyl-tRNA synthetase and an inhibitor in the presence of ATP
keywords	TRNA ligase, Inhibitor, Complex, LIGASE; LIGASE
method	X-RAY DIFFRACTION

▼

Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	32.29 Å
rg_electron	31.80 Å
i0	142346000.00
molecular_weight	96824.0 kDa
excluded_volume	121740 Å³
envelope_volume	153960 Å³
shell_volume	40959 Å³
envelope_diameter	125.9 Å
shell_rg	38.04 Å
envelope_rg	32.38 Å
shape_rg	31.80 Å
total_rg	32.32 Å
total_atoms	6836
n_residues	890
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

▼

3. P(r) Analysis (GNOM)

dmax	120.3 Å
rg_real	32.45 Å
rg_real_error	1.23 Å
i0_real	1.4230e+08
i0_real_error	2.4530e+06
rg_reciprocal	32.38 Å
i0_reciprocal	142300000.0000
total_estimate	0.8278
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	36.8 Å
skewness	0.557
kurtosis	0.232
angular_range	— – 0.2450 Å⁻¹
current_alpha	0.0000
highest_alpha	38250000.0000
n_real_points	50
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.630; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.896; Smooth: 0.970

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (3)

Entity 1 polymer

description	Phenylalanine--tRNA ligase alpha subunit
formula_weight	36433.4 kDa
ec_number	6.1.1.20
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	6836

MGSSHHHHHHKQETELSPEMISSGSWRDRPFKPYNFLAHGVLPDSGHLHPLLKVRSQFRQIFLEMGFTEMPTDNFIESSFWNFDALFQPQQHPARDQHDTFFLRDPAEALQLPMDYVQRVKRTHSQGGYGSQGYKYNWKLDEARKNLLRTHTTSASARALYRLAQKKPFTPVKYFSIDRVFRNETLDATHLAEFHQIEGVVADHGLTLGHLMGVLREFFTKLGITQLRFKPAYNPYTEPSMEVFSYHQGLKKWVEVGNSGVFRPEMLLPMGLPENVSVIAWGLSLERPTMIKYGINNIRELVGHKVNLQMVYDS

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 polymer

description	Phenylalanine--tRNA ligase beta subunit
formula_weight	66214.5 kDa
ec_number	6.1.1.20
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

MPTVSVKRDLLFQALGRTYTDEEFDELCFEFGLELDEITSEKEIISKEQGNVKAAGASDVVLYKIDVPANRYDLLCLEGLVRGLQVFKERIKAPVYKRVMPDGKIQKLIITEETAKIRPFAVAAVLRNIKFTKDRYDSFIELQEKLHQNICRKRALVAIGTHDLDTLSGPFTYTAKRPSDIKFKPLNKTKEYTACELMNIYKTDNHLKHYLHIIENKPLYPVIYDSNGVVLSMPPIINGDHSRITVNTRNIFIECTGTDFTKAKIVLDIIVTMFSEYCENQFTVEAAEVVFPNGKSHTFPELAYRKEMVRADLINKKVGIRETPENLAKLLTRMYLKSEVIGDGNQIEIEIPPTRADIIHACDIVEDAAIAYGYNNIQMTLPKTYTIANQFPLNKLTELLRHDMAAAGFTEALTFALCSQEDIADKLGVDISATKAVHISNPKTAEFQVARTTLLPGLLKTIAANRKMPLPLKLFEISDIVIKDSNTDVGAKNYRHLCAVYYNKNPGFEIIHGLLDRIMQLLDVPPGEDKGGYVIKASEGPAFFPGRCAEIFARGQSVGKLGVLHPDVITKFELTMPCSSLEINIGPFL

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 3 non-polymer

description	[6-(4-CHLOROPHENYL)-2,2-DIMETHYL-7-PHENYL-2,3-DIHYDRO-1H-PYRROLIZIN-5-YL]ACETIC ACID
formula_weight	379.9 kDa
src_method	syn
entity_count	1

▶

6. Citations (1)

▶

length_a	107.904 Å
length_b	107.904 Å
length_c	279.837 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	3.330 Å
resolution_low	48.260 Å
r_factor	0.2222
r_work	0.2193
r_free	0.2557

fit	/app/data/saxs_computation/ud/9udm/9udm.fit
pddf	/app/data/pr_computation/ud/9udm/9udm.pr.out
profile	/app/data/saxs_computation/ud/9udm/9udm.dat

Cocrystal structure of human cytosolic phenylalanyl-tRNA synthetase and an inhibitor in the presence of ATP

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 (3)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)