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1e2h

The nucleoside binding site of Herpes simplex type 1 thymidine kinase analyzed by X-ray crystallography

Method: X-RAY DIFFRACTION D_max: 79.0 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	1e2h
deposition_date	2000-05-23
title	The nucleoside binding site of Herpes simplex type 1 thymidine kinase analyzed by X-ray crystallography
keywords	TRANSFERASE, ADENINE ANALOG, ENZYME-PRODRUG GENE THERAPY, NUCLEOSIDE- BINDING, THYMIDINE KINASE; TRANSFERASE
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	25.59 Å
rg_electron	24.06 Å
i0	72920400.00
molecular_weight	67273.0 kDa
excluded_volume	84515 Å³
envelope_volume	97819 Å³
shell_volume	32659 Å³
envelope_diameter	79.6 Å
shell_rg	32.36 Å
envelope_rg	24.23 Å
shape_rg	24.05 Å
total_rg	24.98 Å
total_atoms	4722
n_residues	617
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	79.0 Å
rg_real	25.44 Å
rg_real_error	0.38 Å
i0_real	7.2920e+07
i0_real_error	1.0080e+06
rg_reciprocal	25.49 Å
i0_reciprocal	72920000.0000
total_estimate	0.7070
solution_quality	REASONABLE a REASONABLE solution
n_peaks	2
r_peak_primary	33.1 Å
skewness	0.141
kurtosis	-0.426
angular_range	— – 0.3100 Å⁻¹
current_alpha	0.0000
highest_alpha	11350000.0000
n_real_points	63
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.911; Stabil: 1.000; Sysdev: 0.164; Positv: 1.000; Valcen: 0.979; Smooth: 0.981

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	THYMIDINE KINASE
formula_weight	35779.1 kDa
ec_number	2.7.1.21
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	4998

MPTLLRVYIDGPHGMGKTTTTQLLVALGSRDDIVYVPEPMTYWRVLGASETIANIYTTQHRLDQGEISAGDAAVVMTSAQITMGMPYAVTDAVLAPHIGGEAGSSHAPPPALTLIFDRHPIAALLCYPAARYLMGSMTPQAVLAFVALIPPTLPGTNIVLGALPEDRHIDRLAKRQRPGERLDLAMLAAIRRVYGLLANTVRYLQCGGSWREDWGQLSGTAVPPQGAEPQSNAGPRPHIGDTLFTLFRAPELLAPNGDLYNVFAWALDVLAKRLRSMHVFILDYDQSPAGCRDALLQLTSGMVQTHVTTPGSIPTICDLARTFAREMGEAN

Source

organism	HERPES SIMPLEX VIRUS (TYPE 1 / STRAIN 17)
ncbi_taxonomy_id	10299
host_organism	ESCHERICHIA COLI

Entity 2 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	2

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	276

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6. Citations (3)

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length_a	113.900 Å
length_b	117.300 Å
length_c	107.900 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	16

space_group	C 2 2 21
int_tables_number	20
crystal_system	—

resolution	1.900 Å
resolution_low	20.000 Å
r_factor	—
r_work	0.2150
r_free	0.2490

fit	/app/data/saxs_computation/e2/1e2h/1e2h.fit
pddf	/app/data/pr_computation/e2/1e2h/1e2h.pr.out
profile	/app/data/saxs_computation/e2/1e2h/1e2h.dat

The nucleoside binding site of Herpes simplex type 1 thymidine kinase analyzed by X-ray crystallography

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