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- PDB-3h3f: Rabbit muscle L-lactate dehydrogenase in complex with NADH and oxamate -

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Basic information

Entry
Database: PDB / ID: 3h3f
TitleRabbit muscle L-lactate dehydrogenase in complex with NADH and oxamate
ComponentsL-lactate dehydrogenase A chain
KeywordsOXIDOREDUCTASE / DEHYDROGENASE / ROSSMANN FOLD / GLYCOLYSIS / NAD / NADH / OXAMATE / M-TYPE TETRAMER
Function / homology
Function and homology information


L-lactate dehydrogenase / lactate metabolic process / L-lactate dehydrogenase activity / pyruvate metabolic process / cytoplasm
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 speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.38 Å
AuthorsBujacz, A. / Bujacz, G. / Swiderek, K. / Paneth, P.
CitationJournal: J.Phys.Chem.B / Year: 2009
Title: Modeling of isotope effects on binding oxamate to lactic dehydrogenase
Authors: Swiderek, K. / Panczakiewicz, A. / Bujacz, A. / Bujacz, G. / Paneth, P.
History
DepositionApr 16, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 15, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Nov 12, 2014Group: Structure summary
Revision 1.3Nov 1, 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 / diffrn_source / 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 / _diffrn_source.pdbx_synchrotron_site / _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)299,24547
Polymers291,8518
Non-polymers7,39439
Water21,5461196
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)149,47521
Polymers145,9264
Non-polymers3,54917
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area28980 Å2
ΔGint-152 kcal/mol
Surface area43650 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)149,77026
Polymers145,9264
Non-polymers3,84522
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area30080 Å2
ΔGint-148 kcal/mol
Surface area43030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.495, 85.279, 138.526
Angle α, β, γ (deg.)98.49, 91.67, 111.59
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
L-lactate dehydrogenase A chain / LDH-A / LDH muscle subunit / LDH-M


Mass: 36481.375 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Details: muscle / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: P13491, 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-OXM / OXAMIC ACID


Mass: 89.050 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H3NO3
#4: Chemical...
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1196 / 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: 2.43 Å3/Da / Density % sol: 49.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 16% PEG 8K, Tris buffer, pH7.5, Sodium acetate 0.1M, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.8162 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Dec 15, 2006
RadiationMonochromator: Si 111 HORIZONTALLY FOCUSING / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8162 Å / Relative weight: 1
ReflectionResolution: 2.38→60 Å / Num. all: 234352 / Num. obs: 98703 / % possible obs: 89.9 % / Observed criterion σ(I): -3 / Redundancy: 2.4 % / Biso Wilson estimate: 34.4 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 10.5
Reflection shellResolution: 2.38→2.47 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.337 / Mean I/σ(I) obs: 2 / Num. unique all: 6121 / % possible all: 55.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.5.0066refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1I10

1i10


Resolution: 2.38→60 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.928 / SU B: 16.33 / SU ML: 0.167 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.85 / ESU R Free: 0.253 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20676 4887 5 %RANDOM
Rwork0.15973 ---
all0.16208 98703 --
obs0.16207 93816 89.65 %-
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: 20.508 Å2
Baniso -1Baniso -2Baniso -3
1-0.56 Å21.3 Å2-0.22 Å2
2--1.83 Å2-0.05 Å2
3----1.46 Å2
Refinement stepCycle: LAST / Resolution: 2.38→60 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20472 0 492 1196 22160
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.02221392
X-RAY DIFFRACTIONr_angle_refined_deg2.0881.9928981
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.59152642
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.21424.994815
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.934153887
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.8871580
X-RAY DIFFRACTIONr_chiral_restr0.1250.23380
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02115452
X-RAY DIFFRACTIONr_mcbond_it0.7291.513192
X-RAY DIFFRACTIONr_mcangle_it1.36221265
X-RAY DIFFRACTIONr_scbond_it2.3538200
X-RAY DIFFRACTIONr_scangle_it3.6254.57715
LS refinement shellResolution: 2.38→2.442 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.363 200 -
Rwork0.284 4001 -
obs--51.18 %
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)
10.5924-0.1114-0.09741.0934-0.03820.7165-0.06830.1025-0.0631-0.14680.0054-0.04860.10970.05380.06290.043-0.00610.02270.0264-0.0070.013812.7778-8.4688-16.1116
20.6293-0.06730.05290.7840.0090.8233-0.05210.0459-0.00120.01140.0250.0336-0.0799-0.08480.02710.01130.0047-0.00210.0143-0.00170.0023-13.142611.9222-13.8193
30.7580.12010.050.6219-0.07890.7582-0.0612-0.0459-0.13380.05380.03220.00980.1345-0.0820.0290.0409-0.00670.02250.01260.00590.0276-7.2747-15.880414.0024
40.5020.21580.1890.61580.00420.6757-0.0572-0.0640.03210.1322-0.0157-0.0298-0.12050.02330.07290.06270.0047-0.02380.0126-0.00050.01098.11813.035216.8772
50.82630.0406-0.01560.93960.49820.7292-0.0622-0.0925-0.08730.1106-0.02070.09870.1302-0.11690.08290.0286-0.00980.02290.0630.00090.0221-39.247114.9198-55.5896
60.6309-0.04870.05180.8497-0.14960.8098-0.0521-0.09240.08210.0528-0.0142-0.0753-0.13830.030.06620.02730.0007-0.01840.0268-0.00740.0193-12.310532.8455-49.6142
70.4864-0.1217-0.04330.70850.010.8348-0.0150.0415-0.0374-0.103-0.0431-0.03580.08080.01830.05810.02490.00680.01350.01490.0010.0095-15.490613.6097-83.9186
80.7409-0.03420.14910.96310.03460.8025-0.06410.11450.1484-0.1179-0.01070.0187-0.1857-0.01730.07480.06050.0091-0.0270.0470.01640.0336-28.494243.5925-81.2807
90.0568-0.02970.01930.2072-0.46661.1724-0.03390.0097-0.00210.0401-0.0146-0.0214-0.06920.01850.04840.0214-0.00840.00020.0135-0.00840.0098-11.786613.3702-34.0619
100.1677-0.07710.22080.2933-0.76482.5433-0.1451-0.00150.05530.0478-0.0647-0.0557-0.079-0.13480.20980.1047-0.0237-0.01340.1166-0.030.0733-11.891413.4072-33.6836
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 95
2X-RAY DIFFRACTION1A96 - 116
3X-RAY DIFFRACTION1A117 - 331
4X-RAY DIFFRACTION2B1 - 331
5X-RAY DIFFRACTION3C1 - 331
6X-RAY DIFFRACTION4D1 - 95
7X-RAY DIFFRACTION4D96 - 116
8X-RAY DIFFRACTION4D117 - 331
9X-RAY DIFFRACTION5E1 - 95
10X-RAY DIFFRACTION5E96 - 116
11X-RAY DIFFRACTION5E117 - 331
12X-RAY DIFFRACTION6F1 - 331
13X-RAY DIFFRACTION7G1 - 331
14X-RAY DIFFRACTION8H1 - 95
15X-RAY DIFFRACTION8H96 - 116
16X-RAY DIFFRACTION8H117 - 331
17X-RAY DIFFRACTION9A332
18X-RAY DIFFRACTION9C332
19X-RAY DIFFRACTION9B332
20X-RAY DIFFRACTION9E332
21X-RAY DIFFRACTION9D332
22X-RAY DIFFRACTION9G332
23X-RAY DIFFRACTION9F332
24X-RAY DIFFRACTION9H332
25X-RAY DIFFRACTION10A333
26X-RAY DIFFRACTION10C333
27X-RAY DIFFRACTION10B333
28X-RAY DIFFRACTION10E333
29X-RAY DIFFRACTION10D333
30X-RAY DIFFRACTION10G333
31X-RAY DIFFRACTION10F333
32X-RAY DIFFRACTION10H333

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