PDB-7dbk: Crystal structure of human LDHB in complex with NADH

ID or keywords:

Entry

Database: PDB / ID: 7dbk

Title

Crystal structure of human LDHB in complex with NADH

Components

L-lactate dehydrogenase B chain

Keywords

OXIDOREDUCTASE / Lactate dehydrogenase / Inhibitor / Complex

Function / homology

Function and homology information

L-lactate dehydrogenase / oxidoreductase complex / NAD metabolic process / Pyruvate metabolism / lactate metabolic process / L-lactate dehydrogenase activity / pyruvate metabolic process / kinase binding / NAD binding / mitochondrial inner membrane ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.802 Å

Authors

Sogabe, S. / Miwa, M.

Citation

Journal: Sci Rep / Year: 2021
Title: Identification of the first highly selective inhibitor of human lactate dehydrogenase B.
Authors: Shibata, S. / Sogabe, S. / Miwa, M. / Fujimoto, T. / Takakura, N. / Naotsuka, A. / Kitamura, S. / Kawamoto, T. / Soga, T.

History

Deposition	Oct 20, 2020	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Oct 20, 2021	Provider: repository / Type: Initial release
Revision 1.1	Nov 10, 2021	Group: Database references / Category: citation Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2	Feb 16, 2022	Group: Database references / Category: citation / citation_author Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3	Nov 29, 2023	Group: Data collection / Derived calculations / Refinement description Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	7dbk.cif.gz	945.6 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	7dbk_validation.pdf.gz	2.5 MB	Display	wwPDB validaton report
Full document	7dbk_full_validation.pdf.gz	2.5 MB	Display
Data in XML	7dbk_validation.xml.gz	101.8 KB	Display
Data in CIF	7dbk_validation.cif.gz	141 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/db/7dbk ftp://data.pdbj.org/pub/pdb/validation_reports/db/7dbk	HTTPS FTP

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Related structure data

Related structure data	7dbjC 1i0zS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	7dbk-2 3h3f-2 4zvv-d 4qo8-d 5w8l-1 7m2n-d 3h3f-1 4qt0-1 4i9h-2 5nqq-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#102 - Jun 2008 Lactate Dehydrogenase similarity (12) #154 - Oct 2012 Citric Acid Cycle similarity (6) #142 - Oct 2011 PDB Pioneers similarity (10) #93 - Sep 2007 Citrate Synthase similarity (1)

Deposited unit

A: L-lactate dehydrogenase B chain

B: L-lactate dehydrogenase B chain

C: L-lactate dehydrogenase B chain

D: L-lactate dehydrogenase B chain

E: L-lactate dehydrogenase B chain

F: L-lactate dehydrogenase B chain

G: L-lactate dehydrogenase B chain

H: L-lactate dehydrogenase B chain

hetero molecules

300 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: L-lactate dehydrogenase B chain

B: L-lactate dehydrogenase B chain

C: L-lactate dehydrogenase B chain

D: L-lactate dehydrogenase B chain

hetero molecules

defined by author&software
150 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

E: L-lactate dehydrogenase B chain

F: L-lactate dehydrogenase B chain

G: L-lactate dehydrogenase B chain

H: L-lactate dehydrogenase B chain

hetero molecules

defined by author&software
150 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	232.477, 84.173, 156.210
Angle α, β, γ (deg.)	90.000, 120.760, 90.000
Int Tables number	5
Space group name H-M	C121

#1: Protein	L-lactate dehydrogenase B chain / LDH-B / LDH heart subunit / LDH-H / Renal carcinoma antigen NY-REN-46 Mass: 36548.207 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: LDHB / Production host: Escherichia coli (E. coli) / References: UniProt: P07195, L-lactate dehydrogenase
#2: Chemical	ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH Mass: 665.441 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₂₁H₂₉N₇O₁₄P₂
#3: Chemical	... ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 977 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.25 Å³/Da / Density % sol: 45.26 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: PEG 3350, ammonium acetate, HEPES

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
Detector	Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 20, 2020
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.8→50 Å / Num. obs: 237609 / % possible obs: 99.6 % / Redundancy: 3.4 % / CC_1/2: 0.994 / R_pim(I) all: 0.042 / R_sym value: 0.065 / Net I/σ(I): 19.8
Reflection shell	Resolution: 1.8→1.83 Å / Mean I/σ(I) obs: 2.1 / Num. unique obs: 11881 / CC_1/2: 0.736 / R_pim(I) all: 0.324 / R_sym value: 0.511 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0266	refinement
HKL-2000		data reduction
SCALEPACK		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1I0Z

1i0z

Resolution: 1.802→49.993 Å / Cor.coef. F_o:F_c: 0.964 / Cor.coef. F_o:F_c free: 0.95 / SU B: 5.666 / SU ML: 0.088 / Cross valid method: FREE R-VALUE / ESU R: 0.125 / ESU R Free: 0.116
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2034	11844	4.985 %
R_work	0.1702	225765	-
all	0.172	-	-
obs	-	237609	99.487 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 29.333 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.578 Å²	-0 Å²	-0.04 Å²
2-	-	0.336 Å²	-0 Å²
3-	-	-	0.17 Å²

Refinement step

Cycle: LAST / Resolution: 1.802→49.993 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	20488	0	484	977	21949

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.013	21310
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	20900
X-RAY DIFFRACTION	r_angle_refined_deg	1.548	1.626	28918
X-RAY DIFFRACTION	r_angle_other_deg	1.373	1.581	48284
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.61	5	2656
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	38.572	24.771	872
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.82	15	3856
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	24.612	15	64
X-RAY DIFFRACTION	r_chiral_restr	0.077	0.2	2856
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	23616
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	4216
X-RAY DIFFRACTION	r_nbd_refined	0.2	0.2	4117
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.178	0.2	19568
X-RAY DIFFRACTION	r_nbtor_refined	0.157	0.2	10255
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.079	0.2	9639
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.136	0.2	969
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.066	0.2	2
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.257	0.2	27
X-RAY DIFFRACTION	r_nbd_other	0.194	0.2	125
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.125	0.2	14
X-RAY DIFFRACTION	r_mcbond_it	1.015	1.672	10648
X-RAY DIFFRACTION	r_mcbond_other	1.015	1.672	10647
X-RAY DIFFRACTION	r_mcangle_it	1.664	2.502	13296
X-RAY DIFFRACTION	r_mcangle_other	1.664	2.503	13297
X-RAY DIFFRACTION	r_scbond_it	1.414	1.937	10662
X-RAY DIFFRACTION	r_scbond_other	1.414	1.937	10663
X-RAY DIFFRACTION	r_scangle_it	2.222	2.822	15622
X-RAY DIFFRACTION	r_scangle_other	2.222	2.822	15623
X-RAY DIFFRACTION	r_lrange_it	4.369	20.519	23209
X-RAY DIFFRACTION	r_lrange_other	4.367	20.506	23199

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.802-1.849	0.269	850	0.238	16434	X-RAY DIFFRACTION	98.1711
1.849-1.899	0.243	831	0.217	16278	X-RAY DIFFRACTION	99.9474
1.899-1.955	0.235	787	0.205	15899	X-RAY DIFFRACTION	99.9641
1.955-2.015	0.231	834	0.185	15368	X-RAY DIFFRACTION	100
2.015-2.081	0.211	755	0.18	14920	X-RAY DIFFRACTION	99.9936
2.081-2.154	0.202	750	0.167	14448	X-RAY DIFFRACTION	100
2.154-2.235	0.22	754	0.168	13946	X-RAY DIFFRACTION	99.9932
2.235-2.326	0.203	715	0.163	13371	X-RAY DIFFRACTION	99.9787
2.326-2.43	0.214	682	0.164	12887	X-RAY DIFFRACTION	99.9632
2.43-2.548	0.203	626	0.16	12332	X-RAY DIFFRACTION	99.9152
2.548-2.686	0.205	611	0.161	11740	X-RAY DIFFRACTION	99.9676
2.686-2.849	0.211	594	0.168	11020	X-RAY DIFFRACTION	99.8281
2.849-3.045	0.224	552	0.166	10384	X-RAY DIFFRACTION	99.7446
3.045-3.289	0.203	491	0.162	9690	X-RAY DIFFRACTION	99.2203
3.289-3.603	0.191	501	0.161	8836	X-RAY DIFFRACTION	99.0453
3.603-4.028	0.186	440	0.161	7999	X-RAY DIFFRACTION	98.437
4.028-4.65	0.165	364	0.15	6926	X-RAY DIFFRACTION	96.4924
4.65-5.694	0.189	339	0.175	5916	X-RAY DIFFRACTION	97.7344
5.694-8.045	0.21	238	0.185	4727	X-RAY DIFFRACTION	99.3199
8.045-49.993	0.187	130	0.178	2644	X-RAY DIFFRACTION	97.6417

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	0.606	0.1372	-0.105	0.7358	0.0675	0.6407	-0.042	0.1031	-0.0018	-0.0882	0.0606	-0.0412	-0.0403	0.0031	-0.0186	0.0179	-0.0198	0.0019	0.0353	0.0048	0.0065	1.225	5.6682	37.0714
2	0.9208	-0.1342	-0.1015	0.5917	0.0956	0.6773	-0.0085	0.1399	-0.0185	-0.0789	0.0017	0.0026	0.0267	-0.0746	0.0067	0.0412	-0.0418	0.0227	0.0702	-0.0334	0.0288	56.6365	24.2986	30.8741

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	A	2 - 334
2	X-RAY DIFFRACTION	1	ALL	B	2 - 334
3	X-RAY DIFFRACTION	1	ALL	C	2 - 334
4	X-RAY DIFFRACTION	1	ALL	D	2 - 334
5	X-RAY DIFFRACTION	2	ALL	E	2 - 334
6	X-RAY DIFFRACTION	2	ALL	F	2 - 334
7	X-RAY DIFFRACTION	2	ALL	G	2 - 334
8	X-RAY DIFFRACTION	2	ALL	H	2 - 334

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