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- PDB-1t2f: Human B lactate dehydrogenase complexed with NAD+ and 4-hydroxy-1... -

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Basic information

Entry
Database: PDB / ID: 1t2f
TitleHuman B lactate dehydrogenase complexed with NAD+ and 4-hydroxy-1,2,5-oxadiazole-3-carboxylic acid
ComponentsL-lactate dehydrogenase B chain
KeywordsOXIDOREDUCTASE / Protein-ligand complex
Function / homology
Function and homology information


L-lactate dehydrogenase / oxidoreductase complex / pyruvate metabolic process / L-lactate dehydrogenase (NAD+) activity / NAD+ metabolic process / Pyruvate metabolism / lactate metabolic process / kinase binding / NAD binding / mitochondrial inner membrane ...L-lactate dehydrogenase / oxidoreductase complex / pyruvate metabolic process / L-lactate dehydrogenase (NAD+) activity / NAD+ metabolic process / Pyruvate metabolism / lactate metabolic process / kinase binding / NAD binding / mitochondrial inner membrane / membrane raft / mitochondrion / extracellular exosome / identical protein binding / membrane / cytoplasm / 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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / 4-HYDROXY-1,2,5-OXADIAZOLE-3-CARBOXYLIC ACID / L-lactate dehydrogenase B chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsCameron, A. / Read, J. / Tranter, R. / Winter, V.J. / Sessions, R.B. / Brady, R.L. / Vivas, L. / Easton, A. / Kendrick, H. / Croft, S.L. ...Cameron, A. / Read, J. / Tranter, R. / Winter, V.J. / Sessions, R.B. / Brady, R.L. / Vivas, L. / Easton, A. / Kendrick, H. / Croft, S.L. / Barros, D. / Lavandera, J.L. / Martin, J.J. / Risco, F. / Garcia-Ochoa, S. / Gamo, F.J. / Sanz, L. / Leon, L. / Ruiz, J.R. / Gabarro, R. / Mallo, A. / De Las Heras, F.G.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Identification and Activity of a Series of Azole-based Compounds with Lactate Dehydrogenase-directed Anti-malarial Activity.
Authors: Cameron, A. / Read, J. / Tranter, R. / Winter, V.J. / Sessions, R.B. / Brady, R.L. / Vivas, L. / Easton, A. / Kendrick, H. / Croft, S.L. / Barros, D. / Lavandera, J.L. / Martin, J.J. / ...Authors: Cameron, A. / Read, J. / Tranter, R. / Winter, V.J. / Sessions, R.B. / Brady, R.L. / Vivas, L. / Easton, A. / Kendrick, H. / Croft, S.L. / Barros, D. / Lavandera, J.L. / Martin, J.J. / Risco, F. / Garcia-Ochoa, S. / Gamo, F.J. / Sanz, L. / Leon, L. / Ruiz, J.R. / Gabarro, R. / Mallo, A. / De Las Heras, F.G.
History
DepositionApr 21, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations / Category: 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
Revision 1.4Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,49512
Polymers146,3214
Non-polymers3,1748
Water4,197233
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25670 Å2
ΔGint-145 kcal/mol
Surface area43360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.397, 160.443, 59.366
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsThe biological assembly is a tetramer

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Components

#1: Protein
L-lactate dehydrogenase B chain / LDH-B / LDH heart subunit / LDH-H


Mass: 36580.293 Da / Num. of mol.: 4 / Mutation: D332F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LDHB / Plasmid: pKK223 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P07195, L-lactate dehydrogenase
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical
ChemComp-OXQ / 4-HYDROXY-1,2,5-OXADIAZOLE-3-CARBOXYLIC ACID


Mass: 130.059 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H2N2O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 233 / 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: 2.18 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 4000, Ammonium acetate, Na citrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418 Å
DetectorType: MACSCIENCE / Detector: IMAGE PLATE / Date: Jul 11, 2001
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3→30 Å / Num. all: 27214 / Num. obs: 24742 / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.7 % / Rsym value: 0.166 / Net I/σ(I): 6.4
Reflection shellResolution: 3→3.16 Å / Mean I/σ(I) obs: 2.6 / Rsym value: 0.302 / % possible all: 79.1

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Processing

Software
NameVersionClassification
REFMAC5refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1IOZ

1ioz


Resolution: 3→29.88 Å / Cor.coef. Fo:Fc: 0.905 / Cor.coef. Fo:Fc free: 0.78 / SU B: 30.005 / SU ML: 0.55 / Cross valid method: THROUGHOUT / ESU R Free: 0.675 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.32053 1242 5.1 %RANDOM
Rwork0.21527 ---
obs0.2206 23299 90.52 %-
all-24474 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 52.254 Å2
Baniso -1Baniso -2Baniso -3
1--2.42 Å20 Å20 Å2
2--2.71 Å20 Å2
3----0.29 Å2
Refinement stepCycle: LAST / Resolution: 3→29.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10220 0 212 233 10665
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.02110348
X-RAY DIFFRACTIONr_bond_other_d0.0020.029507
X-RAY DIFFRACTIONr_angle_refined_deg2.0171.98514084
X-RAY DIFFRACTIONr_angle_other_deg1.381322109
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.00151324
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1180.21670
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211360
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021834
X-RAY DIFFRACTIONr_nbd_refined0.2660.23258
X-RAY DIFFRACTIONr_nbd_other0.2540.212752
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0920.26651
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2580.2442
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.2020.534
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3110.224
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3320.250
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2750.29
X-RAY DIFFRACTIONr_symmetry_hbond_other0.0840.52
X-RAY DIFFRACTIONr_mcbond_it0.6331.56552
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.161210559
X-RAY DIFFRACTIONr_scbond_it1.55433796
X-RAY DIFFRACTIONr_scangle_it2.6684.53525
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.995→3.072 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.384 68
Rwork0.26 1370

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