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- PDB-1i10: HUMAN MUSCLE L-LACTATE DEHYDROGENASE M CHAIN, TERNARY COMPLEX WIT... -

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Basic information

Entry
Database: PDB / ID: 1i10
TitleHUMAN MUSCLE L-LACTATE DEHYDROGENASE M CHAIN, TERNARY COMPLEX WITH NADH AND OXAMATE
ComponentsL-LACTATE DEHYDROGENASE M CHAIN
KeywordsOXIDOREDUCTASE / DEHYDROGENASE / ROSSMANN FOLD
Function / homology
Function and homology information


L-lactate dehydrogenase / oxidoreductase complex / L-lactate dehydrogenase (NAD+) activity / Pyruvate metabolism / lactate metabolic process / pyruvate metabolic process / substantia nigra development / Regulation of pyruvate metabolism / glycolytic process / cadherin binding ...L-lactate dehydrogenase / oxidoreductase complex / L-lactate dehydrogenase (NAD+) activity / Pyruvate metabolism / lactate metabolic process / pyruvate metabolic process / substantia nigra development / Regulation of pyruvate metabolism / glycolytic process / cadherin binding / mitochondrion / extracellular exosome / identical protein binding / nucleus / membrane / 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
ACETATE ION / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / OXAMIC ACID / L-lactate dehydrogenase A chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsRead, J.A. / Winter, V.J. / Eszes, C.M. / Sessions, R.B. / Brady, R.L.
CitationJournal: Proteins / Year: 2001
Title: Structural basis for altered activity of M- and H-isozyme forms of human lactate dehydrogenase.
Authors: Read, J.A. / Winter, V.J. / Eszes, C.M. / Sessions, R.B. / Brady, R.L.
History
DepositionJan 30, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 28, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 12, 2014Group: Structure summary
Revision 1.4Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 M CHAIN
B: L-LACTATE DEHYDROGENASE M CHAIN
C: L-LACTATE DEHYDROGENASE M CHAIN
D: L-LACTATE DEHYDROGENASE M CHAIN
E: L-LACTATE DEHYDROGENASE M CHAIN
F: L-LACTATE DEHYDROGENASE M CHAIN
G: L-LACTATE DEHYDROGENASE M CHAIN
H: L-LACTATE DEHYDROGENASE M CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)299,33632
Polymers292,8288
Non-polymers6,50824
Water11,746652
1
A: L-LACTATE DEHYDROGENASE M CHAIN
B: L-LACTATE DEHYDROGENASE M CHAIN
C: L-LACTATE DEHYDROGENASE M CHAIN
D: L-LACTATE DEHYDROGENASE M CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,66816
Polymers146,4144
Non-polymers3,25412
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27650 Å2
ΔGint-152 kcal/mol
Surface area42700 Å2
MethodPISA
2
E: L-LACTATE DEHYDROGENASE M CHAIN
F: L-LACTATE DEHYDROGENASE M CHAIN
G: L-LACTATE DEHYDROGENASE M CHAIN
H: L-LACTATE DEHYDROGENASE M CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,66816
Polymers146,4144
Non-polymers3,25412
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27820 Å2
ΔGint-155 kcal/mol
Surface area42720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.942, 158.542, 266.226
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is composed of subunits A, B, C and D or E, F, G and H

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Components

#1: Protein
L-LACTATE DEHYDROGENASE M CHAIN / LDH-A


Mass: 36603.473 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LDHA / Organ: HEART / Plasmid: PKK223-3 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P00338, L-lactate dehydrogenase
#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical
ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH


Mass: 665.441 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C21H29N7O14P2
#4: Chemical
ChemComp-OXM / OXAMIC ACID


Mass: 89.050 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H3NO3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 652 / 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: 2.34 Å3/Da / Density % sol: 47.42 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: protein solution: 28 mg/ml protein, 100 mM Na-HEPES pH 7.5, 2.5 mM NADH, 1 mM Na Oxamate. Well solution: 12% PEG 8K, 100 mM Na HEPES pH 7.5, 100 mM Na Acetate, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
Temperature: 18 ℃
Details: drop consists of equal amounts of protein and reservoir solutions
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
128 mg/mlprotein1drop
22.5 mMNADH1drop
31 mMsodium oxamate1drop
4100 mMHEPES1drop
512 %PEG80001reservoir
6100 mMsodium acetate1reservoir
7100 mMsodium HEPES1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX7.2 / Wavelength: 1.488
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 13, 1999
RadiationMonochromator: platinum mirrors/Ge 111 monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. all: 121781 / Num. obs: 112344 / % possible obs: 92.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.51 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 14.18
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 3.53 % / Rmerge(I) obs: 0.195 / Mean I/σ(I) obs: 5.36 / Num. unique all: 13397 / % possible all: 89
Reflection shell
*PLUS
% possible obs: 89 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 9ldt

9ldt


Resolution: 2.3→20 Å / SU B: 8.643 / SU ML: 0.211 / SU Rfree: 0.279 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.487 / ESU R Free: 0.279 / Stereochemistry target values: ENGH AND HUBER
Details: Scaling details: Babinet's principle for scaling has been used. Bulk solvent correction based on constant value has been used. Parameters for mask calculation: VDW prob radii = 1.40; ION ...Details: Scaling details: Babinet's principle for scaling has been used. Bulk solvent correction based on constant value has been used. Parameters for mask calculation: VDW prob radii = 1.40; ION prob radii = 0.80; Shrinkage radii = 0.80. CNS was also used for refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.25713 5577 5 %RANDOM
Rwork0.19722 ---
obs0.20024 105591 90.5 %-
Displacement parametersBiso mean: 27.066 Å2
Baniso -1Baniso -2Baniso -3
1--0.19 Å20 Å20 Å2
2--1.02 Å20 Å2
3----0.83 Å2
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20497 0 432 653 21582
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0170.022
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.8151.992
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it0.8431.5
X-RAY DIFFRACTIONp_mcangle_it1.5442
X-RAY DIFFRACTIONp_scbond_it2.5163
X-RAY DIFFRACTIONp_scangle_it3.9494.5
X-RAY DIFFRACTIONp_plane_restr0.0060.02
X-RAY DIFFRACTIONp_chiral_restr0.1190.2
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1720.5
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.2 / Rfactor Rfree: 0.257 / Rfactor Rwork: 0.197
Solvent computation
*PLUS
Displacement parameters
*PLUS

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