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- PDB-4qsm: Crystal structure of human muscle L-lactate dehydrogenase in comp... -

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Basic information

Entry
Database: PDB / ID: 4qsm
TitleCrystal structure of human muscle L-lactate dehydrogenase in complex with inhibitor 2, 3-{[7-(2,4-dimethoxypyrimidin-5-yl)-3-sulfamoylquinolin-4-yl]amino}benzoic acid
ComponentsL-lactate dehydrogenase A chain
Keywordsoxidoreductase/oxidoreductase Inhibitor / Rossmann Fold / oxidoreductase-oxidoreductase Inhibitor complex
Function / homology
Function and homology information


oxidoreductase complex / Pyruvate metabolism / L-lactate dehydrogenase / lactate metabolic process / L-lactate dehydrogenase activity / pyruvate metabolic process / substantia nigra development / glycolytic process / cadherin binding / mitochondrion ...oxidoreductase complex / Pyruvate metabolism / L-lactate dehydrogenase / lactate metabolic process / L-lactate dehydrogenase activity / pyruvate metabolic process / substantia nigra development / glycolytic process / cadherin binding / mitochondrion / extracellular exosome / identical protein binding / membrane / nucleus / cytosol
Similarity search - Function
L-lactate dehydrogenase / L-lactate dehydrogenase active site. / L-lactate dehydrogenase, active site / L-2-Hydroxyisocaproate Dehydrogenase; Chain A, domain 2 / Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal / L-lactate/malate dehydrogenase / Lactate/malate dehydrogenase, N-terminal / Lactate/malate dehydrogenase, C-terminal / lactate/malate dehydrogenase, NAD binding domain / lactate/malate dehydrogenase, alpha/beta C-terminal domain ...L-lactate dehydrogenase / L-lactate dehydrogenase active site. / L-lactate dehydrogenase, active site / L-2-Hydroxyisocaproate Dehydrogenase; Chain A, domain 2 / Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal / L-lactate/malate dehydrogenase / Lactate/malate dehydrogenase, N-terminal / Lactate/malate dehydrogenase, C-terminal / lactate/malate dehydrogenase, NAD binding domain / lactate/malate dehydrogenase, alpha/beta C-terminal domain / Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-38K / L-lactate dehydrogenase A chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsKolappan, S. / Craig, L.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2015
Title: Structures of lactate dehydrogenase A (LDHA) in apo, ternary and inhibitor-bound forms.
Authors: Kolappan, S. / Shen, D.L. / Mosi, R. / Sun, J. / McEachern, E.J. / Vocadlo, D.J. / Craig, L.
History
DepositionJul 6, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 3, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 25, 2015Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: L-lactate dehydrogenase A chain
B: L-lactate dehydrogenase A chain
C: L-lactate dehydrogenase A chain
D: L-lactate dehydrogenase A chain
E: L-lactate dehydrogenase A chain
F: L-lactate dehydrogenase A chain
G: L-lactate dehydrogenase A chain
H: L-lactate dehydrogenase A chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)303,31116
Polymers299,4598
Non-polymers3,8528
Water1,08160
1
A: L-lactate dehydrogenase A chain
B: L-lactate dehydrogenase A chain
C: L-lactate dehydrogenase A chain
D: L-lactate dehydrogenase A chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,6558
Polymers149,7294
Non-polymers1,9264
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21350 Å2
ΔGint-131 kcal/mol
Surface area47170 Å2
MethodPISA
2
E: L-lactate dehydrogenase A chain
F: L-lactate dehydrogenase A chain
G: L-lactate dehydrogenase A chain
H: L-lactate dehydrogenase A chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,6558
Polymers149,7294
Non-polymers1,9264
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21130 Å2
ΔGint-138 kcal/mol
Surface area47150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)147.310, 147.310, 334.490
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein
L-lactate dehydrogenase A chain / LDH-A / Cell proliferation-inducing gene 19 protein / LDH muscle subunit / LDH-M / Renal carcinoma ...LDH-A / Cell proliferation-inducing gene 19 protein / LDH muscle subunit / LDH-M / Renal carcinoma antigen NY-REN-59


Mass: 37432.344 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LDHA, PIG19 / Production host: Escherichia coli (E. coli) / References: UniProt: P00338, L-lactate dehydrogenase
#2: Chemical
ChemComp-38K / 3-{[7-(2,4-dimethoxypyrimidin-5-yl)-3-sulfamoylquinolin-4-yl]amino}benzoic acid


Mass: 481.481 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C22H19N5O6S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.5 Å3/Da / Density % sol: 64.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7
Details: 50 mM LiCl, PEG400 41 % w/v, 100 mM Bis-tris propane, pH 7.0, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 2, 2013 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→35 Å / Num. all: 85010 / Num. obs: 84925 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allDiffraction-ID% possible all
3.03-3.087.51.022.24419199.9
3.08-3.147.50.8782.54400199.9
3.14-3.217.50.7932.84260199.9
3.21-3.277.50.6723.24204199.9
3.27-3.357.50.534.14125199.9
3.35-3.427.50.4514.84048199.9
3.42-3.517.50.3925.63922199.9
3.51-3.597.50.3346.53887199.9
3.59-3.697.50.2957.33778199.9
3.69-3.797.50.2458.73651199.9
3.79-3.917.50.211103605199.9
3.91-4.037.50.17611.83465199.8
4.03-4.177.40.15213.23376199.8
4.17-4.327.40.1216.33274199.8
4.32-4.497.40.09520.23139199.8
4.49-4.687.40.081233073199.8
4.68-4.97.40.077242875199.7
4.9-5.157.30.07424.22809199.7
5.15-5.447.20.07922.82678199.6
5.44-5.87.20.08820.12535199.6
5.8-6.237.10.07821.52370199.5
6.23-6.777.40.06425.62248199.4
6.77-7.487.40.05926.82072199.3
7.48-8.497.30.04136.71875199
8.49-10.047.20.03148.71678198.6
10.04-12.967.10.02459.41426197.9
12.96-22.456.90.024561135196.2
22.45-3560.02546.8598189.3

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Processing

Software
NameVersionClassification
Blu-Icedata collection
REFMAC5.7.0029refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→34.62 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.873 / SU B: 30.17 / SU ML: 0.251 / Cross valid method: THROUGHOUT / ESU R Free: 0.387 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.247 4518 5.3 %RANDOM
Rwork0.167 ---
obs0.172 80339 99.88 %-
all-84925 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 65.878 Å2
Baniso -1Baniso -2Baniso -3
1--1.38 Å2-1.38 Å20 Å2
2---1.38 Å20 Å2
3---4.48 Å2
Refinement stepCycle: LAST / Resolution: 3→34.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20566 0 272 60 20898
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01921494
X-RAY DIFFRACTIONr_bond_other_d0.0020.0221311
X-RAY DIFFRACTIONr_angle_refined_deg1.5511.98629149
X-RAY DIFFRACTIONr_angle_other_deg0.839349109
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.43952701
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.6225.114833
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.922153979
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1421590
X-RAY DIFFRACTIONr_chiral_restr0.0780.23361
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0223987
X-RAY DIFFRACTIONr_gen_planes_other0.0070.024573
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3→3.077 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 308 -
Rwork0.261 5836 -
obs--99.97 %
Refinement TLS params.

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

IDL11 (°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)
11.5691-0.08770.01611.4098-0.0291.15860.0010.2525-0.2719-0.2235-0.0102-0.12560.1430.10440.00920.2481-0.07010.00590.2092-0.0950.090570.7292-23.3529-29.3494
22.05520.0121-0.12292.2754-0.15880.4561-0.01440.26110.1128-0.3079-0.02650.5213-0.098-0.22380.04090.2559-0.0528-0.0940.2189-0.03750.143145.0715-2.7991-22.985
31.12390.2762-0.43991.79280.16111.99890.0128-0.1518-0.06980.452-0.0392-0.10450.02080.10280.02640.3076-0.1176-0.08490.09920.04310.030169.784-12.55566.6343
42.05160.59220.35922.0974-0.70531.0192-0.0440.0860.23750.0443-0.0409-0.194-0.22040.04210.08480.2649-0.1019-0.03960.1450.02550.08478.19612.467-13.698
52.56080.2539-0.35221.5936-0.12711.4537-0.09370.69530.0176-0.56910.11380.3333-0.001-0.2157-0.02020.4907-0.0951-0.19610.46720.01710.092110.4238-53.0431-80.446
61.8010.5471-0.17482.71730.08651.0665-0.0217-0.1192-0.15920.088-0.03350.24120.0758-0.15220.05510.2531-0.0878-0.05590.2517-0.00580.074110.8947-69.558-51.2789
72.27860.1527-0.06281.33520.05131.02750.01490.16180.2418-0.18920.1027-0.1669-0.03550.151-0.11760.2435-0.04890.00410.1638-0.03760.072641.7088-46.5681-60.9376
81.91180.2635-0.21321.8377-0.02541.05670.0048-0.21910.62560.151-0.00910.2451-0.1855-0.19880.00430.27430.0059-0.0750.2597-0.10350.263514.7886-32.5634-46.4347
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 333
2X-RAY DIFFRACTION2B2 - 332
3X-RAY DIFFRACTION3C2 - 333
4X-RAY DIFFRACTION4D2 - 333
5X-RAY DIFFRACTION5E2 - 332
6X-RAY DIFFRACTION6F2 - 332
7X-RAY DIFFRACTION7G2 - 332
8X-RAY DIFFRACTION8H2 - 332

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