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- PDB-2dld: D-LACTATE DEHYDROGENASE COMPLEXED WITH NADH AND OXAMATE -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 2dld
TitleD-LACTATE DEHYDROGENASE COMPLEXED WITH NADH AND OXAMATE
ComponentsD-LACTATE DEHYDROGENASE
KeywordsOXIDOREDUCTASE (CHOH(D)-NAD+(A))
Function / homology
Function and homology information


D-lactate dehydrogenase / D-lactate dehydrogenase activity / NAD binding
Similarity search - Function
D-isomer specific 2-hydroxyacid dehydrogenases signature 2. / D-isomer specific 2-hydroxyacid dehydrogenases NAD-binding signature. / D-isomer specific 2-hydroxyacid dehydrogenases signature 3. / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site 1 / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site / D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain / D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain / D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain / NAD(P)-binding Rossmann-like Domain ...D-isomer specific 2-hydroxyacid dehydrogenases signature 2. / D-isomer specific 2-hydroxyacid dehydrogenases NAD-binding signature. / D-isomer specific 2-hydroxyacid dehydrogenases signature 3. / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site 1 / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site / D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain / D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain / D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / OXAMIC ACID / D-lactate dehydrogenase
Similarity search - Component
Biological speciesLactobacillus helveticus (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.7 Å
AuthorsDunn, C.R. / Holbrook, J.J.
CitationJournal: To be Published
Title: Dehydrogenases Engineering to Correct Substrate Inhibition in a Commercial Dehydrogenase
Authors: Bernard, N. / Delcour, J. / Alvarez, A. / Cortes, A. / Willis, C. / Holbrook, J.J.
History
DepositionOct 28, 1995Processing site: BNL
Revision 1.0Mar 14, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 6, 2013Group: Non-polymer description
Revision 1.4Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_conn.pdbx_leaving_atom_flag / _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: D-LACTATE DEHYDROGENASE
B: D-LACTATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,1716
Polymers75,6622
Non-polymers1,5094
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8590 Å2
ΔGint-21 kcal/mol
Surface area27870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.200, 62.100, 77.400
Angle α, β, γ (deg.)90.00, 113.20, 90.00
Int Tables number4
Space group name H-MP1211
Atom site foot note1: CIS PROLINE - PRO A 138 / 2: CIS PROLINE - PRO B 138

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Components

#1: Protein D-LACTATE DEHYDROGENASE / / R-LACTATE DEHYDROGENASE


Mass: 37831.141 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: CRYSTALLIZED IN 11% PEG 4000, 5 MM BIS-TRIS PH 6.8, 75 MG/ML ENZYME, 3 MM NADH, 10 MM OXAMATE
Source: (natural) Lactobacillus helveticus (bacteria) / References: UniProt: P30901, D-lactate dehydrogenase
#2: Chemical ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH / Nicotinamide adenine dinucleotide


Mass: 665.441 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H29N7O14P2
#3: Chemical ChemComp-OXM / OXAMIC ACID / Oxamic acid


Mass: 89.050 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3NO3

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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: 2.52 Å3/Da / Density % sol: 51.11 %
Crystal growpH: 6.8 / Details: pH 6.8

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Data collection

Diffraction sourceWavelength: 1.5418 Å
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Dec 7, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→48 Å / Num. obs: 18315 / % possible obs: 89 % / Observed criterion σ(I): 0 / Redundancy: 3 % / Rmerge(I) obs: 0.065

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Processing

Software
NameClassification
PROLSQrefinement
XENGENdata reduction
RefinementResolution: 2.7→10 Å / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.297 --
obs0.195 16190 82 %
Displacement parametersBiso mean: 35 Å2
Refinement stepCycle: LAST / Resolution: 2.7→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5316 0 100 0 5416
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.020.02
X-RAY DIFFRACTIONp_angle_d0.0290.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0490.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.82
X-RAY DIFFRACTIONp_mcangle_it3.12.5
X-RAY DIFFRACTIONp_scbond_it2.42.5
X-RAY DIFFRACTIONp_scangle_it3.93
X-RAY DIFFRACTIONp_plane_restr0.0190.02
X-RAY DIFFRACTIONp_chiral_restr0.160.15
X-RAY DIFFRACTIONp_singtor_nbd0.250.5
X-RAY DIFFRACTIONp_multtor_nbd0.360.5
X-RAY DIFFRACTIONp_xhyhbond_nbd0.330.5
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor2.63
X-RAY DIFFRACTIONp_staggered_tor2715
X-RAY DIFFRACTIONp_orthonormal_tor37.620
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor

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