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- PDB-9ayi: Human malic enzyme 2 cofactor complex at 1.89 Angstrom. -

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Basic information

Entry
Database: PDB / ID: 9ayi
TitleHuman malic enzyme 2 cofactor complex at 1.89 Angstrom.
ComponentsNAD-dependent malic enzyme, mitochondrial
KeywordsOXIDOREDUCTASE / Malic enzyme 2 / NAD+ / co-factor complex / ME2 / mitochondrial localisation / m-NAD-ME
Function / homology
Function and homology information


malate dehydrogenase (oxaloacetate-decarboxylating) / regulation of NADP metabolic process / malate dehydrogenase (decarboxylating) (NAD+) activity / malic enzyme activity / malate dehydrogenase (decarboxylating) (NADP+) activity / oxaloacetate decarboxylase activity / malate metabolic process / Pyruvate metabolism / pyruvate metabolic process / Mitochondrial protein degradation ...malate dehydrogenase (oxaloacetate-decarboxylating) / regulation of NADP metabolic process / malate dehydrogenase (decarboxylating) (NAD+) activity / malic enzyme activity / malate dehydrogenase (decarboxylating) (NADP+) activity / oxaloacetate decarboxylase activity / malate metabolic process / Pyruvate metabolism / pyruvate metabolic process / Mitochondrial protein degradation / NAD binding / electron transfer activity / mitochondrial matrix / intracellular membrane-bounded organelle / mitochondrion / metal ion binding
Similarity search - Function
Malic enzyme, conserved site / Malic enzymes signature. / Malic oxidoreductase / Malic enzyme, N-terminal domain / Malic enzyme, N-terminal domain / Malic enzyme, NAD-binding / Malic enzyme, N-terminal domain superfamily / Malic enzyme, N-terminal domain / Malic enzyme, NAD binding domain / Malic enzyme, NAD binding domain ...Malic enzyme, conserved site / Malic enzymes signature. / Malic oxidoreductase / Malic enzyme, N-terminal domain / Malic enzyme, N-terminal domain / Malic enzyme, NAD-binding / Malic enzyme, N-terminal domain superfamily / Malic enzyme, N-terminal domain / Malic enzyme, NAD binding domain / Malic enzyme, NAD binding domain / Aminoacid dehydrogenase-like, N-terminal domain superfamily / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / L(+)-TARTARIC ACID / NAD-dependent malic enzyme, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsKrinkel, B.A. / Squire, C.J. / Loomes, K.M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Human malic enzyme 2 complex with inhibitor NPD-389
Authors: Krinkel, B.A. / Squire, C.J. / Loomes, K.M.
History
DepositionMar 7, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 12, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NAD-dependent malic enzyme, mitochondrial
B: NAD-dependent malic enzyme, mitochondrial
C: NAD-dependent malic enzyme, mitochondrial
D: NAD-dependent malic enzyme, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)265,23427
Polymers258,8254
Non-polymers6,40923
Water35,3091960
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area29340 Å2
ΔGint-160 kcal/mol
Surface area78460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.325, 98.166, 107.739
Angle α, β, γ (deg.)65.32, 70.75, 74.89
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
NAD-dependent malic enzyme, mitochondrial / NAD-ME / Malic enzyme 2


Mass: 64706.309 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ME2 / Production host: Escherichia coli (E. coli)
References: UniProt: P23368, malate dehydrogenase (oxaloacetate-decarboxylating)

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Non-polymers , 6 types, 1983 molecules

#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical
ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H6O6
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1960 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationY

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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: 2.67 Å3/Da / Density % sol: 53.87 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M Bis-Tris, 0.1 M Ammonium Tartrate, 0.02 M Potassium Citrate, 20% PEG-3350.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 7, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.89→47.42 Å / Num. obs: 200119 / % possible obs: 98.2 % / Redundancy: 3.6 % / CC1/2: 0.99 / Net I/σ(I): 6.9
Reflection shellResolution: 1.89→1.93 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 1.6 / Num. unique obs: 8176 / CC1/2: 0.483 / % possible all: 79.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.89→47.42 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.954 / SU B: 3.54 / SU ML: 0.1 / Cross valid method: THROUGHOUT / ESU R: 0.148 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20096 10256 5.1 %RANDOM
Rwork0.17712 ---
obs0.17836 189840 97.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.068 Å2
Baniso -1Baniso -2Baniso -3
1-0.76 Å21.56 Å2-1.51 Å2
2---0.49 Å2-0.36 Å2
3----0.27 Å2
Refinement stepCycle: 1 / Resolution: 1.89→47.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17334 0 418 1960 19712
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.01218553
X-RAY DIFFRACTIONr_bond_other_d0.0010.01617534
X-RAY DIFFRACTIONr_angle_refined_deg1.0941.83225229
X-RAY DIFFRACTIONr_angle_other_deg0.4041.75440423
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.79252270
X-RAY DIFFRACTIONr_dihedral_angle_2_deg4.5625137
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.727103104
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0560.22816
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0221632
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024221
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_it1.3913.058993
X-RAY DIFFRACTIONr_mcbond_other1.3913.058993
X-RAY DIFFRACTIONr_mcangle_it2.2945.47811265
X-RAY DIFFRACTIONr_mcangle_other2.2945.47911266
X-RAY DIFFRACTIONr_scbond_it1.7913.3119560
X-RAY DIFFRACTIONr_scbond_other1.7913.3119561
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.0366.00413956
X-RAY DIFFRACTIONr_long_range_B_refined5.1730.9821340
X-RAY DIFFRACTIONr_long_range_B_other4.98229.5820841
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.893→1.942 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 713 -
Rwork0.286 12285 -
obs--85.34 %

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