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9udl

Cocrystal structure of human cytosolic phenylalanyl-tRNA synthetase and an inhibitor

Method: X-RAY DIFFRACTION D_max: 120.7 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9udl
deposition_date	2025-04-07
last_revision	2026-04-15
title	Cocrystal structure of human cytosolic phenylalanyl-tRNA synthetase and an inhibitor
keywords	TRNA ligase, Inhibitor, Complex, 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	32.39 Å
rg_electron	31.90 Å
i0	142319000.00
molecular_weight	96824.0 kDa
excluded_volume	121740 Å³
envelope_volume	154900 Å³
shell_volume	41104 Å³
envelope_diameter	126.4 Å
shell_rg	38.12 Å
envelope_rg	32.47 Å
shape_rg	31.91 Å
total_rg	32.42 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

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3. P(r) Analysis (GNOM)

dmax	120.7 Å
rg_real	32.55 Å
rg_real_error	0.98 Å
i0_real	1.4230e+08
i0_real_error	2.1040e+06
rg_reciprocal	32.48 Å
i0_reciprocal	142300000.0000
total_estimate	0.8278
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	37.0 Å
skewness	0.559
kurtosis	0.233
angular_range	— – 0.2450 Å⁻¹
current_alpha	0.0000
highest_alpha	39070000.0000
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: 0.971

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4. Crystallography & Experiment

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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

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6. Citations (1)

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length_a	109.352 Å
length_b	109.352 Å
length_c	279.959 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	3.400 Å
resolution_low	45.350 Å
r_factor	0.2184
r_work	0.2170
r_free	0.2435

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

Cocrystal structure of human cytosolic phenylalanyl-tRNA synthetase and an inhibitor

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)