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9qyk

Crystal structure of human L-lactate Dehydrogenase B protein in complex with NADH, oxamate and sertraline

Method: X-RAY DIFFRACTION D_max: 98.5 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9qyk
deposition_date	2025-04-18
last_revision	2026-04-29
title	Crystal structure of human L-lactate Dehydrogenase B protein in complex with NADH, oxamate and sertraline
keywords	Sertraline, modulator, complex, OXIDOREDUCTASE; OXIDOREDUCTASE
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	32.83 Å
rg_electron	31.71 Å
i0	343313000.00
molecular_weight	151710.0 kDa
excluded_volume	191240 Å³
envelope_volume	230710 Å³
shell_volume	56882 Å³
envelope_diameter	104.0 Å
shell_rg	41.25 Å
envelope_rg	31.91 Å
shape_rg	31.74 Å
total_rg	32.34 Å
total_atoms	10773
n_residues	1353
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	98.5 Å
rg_real	32.56 Å
rg_real_error	0.42 Å
i0_real	3.4330e+08
i0_real_error	4.4970e+06
rg_reciprocal	32.67 Å
i0_reciprocal	343300000.0000
total_estimate	0.9035
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	1
r_peak_primary	43.1 Å
skewness	0.091
kurtosis	-0.551
angular_range	— – 0.2400 Å⁻¹
current_alpha	0.0000
highest_alpha	176200000.0000
n_real_points	49
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.942; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.974; Smooth: 0.940

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	L-lactate dehydrogenase B chain
formula_weight	38471.2 kDa
ec_number	1.1.1.27
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	A,B,C,D
atom_count	11703

ATLKEKLIAPVAEEEATVPNNKITVVGVGQVGMACAISILGKSLADELALVDVLEDKLKGEMMDLQHGSLFLQTPKIVADKDYSVTANSKIVVVTAGVRQQEGESRLNLVQRNVNVFKFIIPQIVKYSPDCIIIVVSNPVDILTYVTWKLSGLPKHRVIGSGCNLDSARFRYLMAEKLGIHPSSCHGWILGEHGDSSVAVWSGVNVAGVSLQELNPEMGTDNDSENWKEVHKMVVESAYEVIKLKGYTNWAIGLSVADLIESMLKNLSRIHPVSTMVKGMYGIENEVFLSLPCILNARGLTSVINQKLKDDEVAQLKKSADTLWDIQKDLKDLENLYFQGLEHHHHHH

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	OXAMIC ACID
formula_weight	89.0 kDa
src_method	syn
entity_count	3

Entity 3 non-polymer

description	1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
formula_weight	665.4 kDa
src_method	syn
entity_count	3

Entity 4 non-polymer

description	(1S,4S)-4-(3,4-dichlorophenyl)-N-methyl-1,2,3,4-tetrahydronaphthalen-1-amine
formula_weight	306.2 kDa
src_method	syn
entity_count	3

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	868

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6. Citations (1)

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length_a	84.760 Å
length_b	119.350 Å
length_c	159.090 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	16

space_group	P 21 21 21
int_tables_number	19
crystal_system	orthorhombic

resolution	2.060 Å
resolution_low	48.790 Å
r_factor	0.1745
r_work	0.1724
r_free	0.2156

fit	/app/data/saxs_computation/qy/9qyk/9qyk.fit
pddf	/app/data/pr_computation/qy/9qyk/9qyk.pr.out
profile	/app/data/saxs_computation/qy/9qyk/9qyk.dat