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- PDB-9cmq: Horse liver alcohol dehydrogenase V203A in complex with NADH and ... -

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Basic information

Entry
Database: PDB / ID: 9cmq
TitleHorse liver alcohol dehydrogenase V203A in complex with NADH and N-cylcohexyl formamide
ComponentsAlcohol dehydrogenase E chain
KeywordsOXIDOREDUCTASE / Inhibitor
Function / homology
Function and homology information


all-trans-retinol dehydrogenase (NAD+) activity / alcohol dehydrogenase / retinoic acid metabolic process / retinol metabolic process / zinc ion binding / cytosol
Similarity search - Function
Alcohol dehydrogenase, zinc-type, conserved site / Zinc-containing alcohol dehydrogenases signature. / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / Polyketide synthase, enoylreductase domain / Enoylreductase / GroES-like superfamily / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
CYCLOHEXYLFORMAMIDE / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / Alcohol dehydrogenase E chain
Similarity search - Component
Biological speciesEquus caballus (horse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 Å
AuthorsMukherjee, S. / Boxer, S.G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/Office of the DirectorR35GM118044 United States
CitationJournal: To Be Published
Title: Role of Electrostatics in Hydride Transfer by Horse liver alcohol dehydrogenase
Authors: Mukherjee, S. / Fried, S.D.E. / Boxer, S.G.
History
DepositionJul 15, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 16, 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: Alcohol dehydrogenase E chain
B: Alcohol dehydrogenase E chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,86810
Polymers80,0212
Non-polymers1,8478
Water11,656647
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7040 Å2
ΔGint-107 kcal/mol
Surface area26240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.243, 50.508, 92.812
Angle α, β, γ (deg.)92.34, 103.03, 109.22
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Alcohol dehydrogenase E chain


Mass: 40010.398 Da / Num. of mol.: 2 / Mutation: V203A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Equus caballus (horse) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P00327, alcohol dehydrogenase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH


Mass: 665.441 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H29N7O14P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CXF / CYCLOHEXYLFORMAMIDE


Mass: 127.184 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H13NO / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 647 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.37 Å3/Da / Density % sol: 48.01 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: PEG 400, Tris Buffer / Temp details: Cold Room

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-1 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 24, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.49→34.8 Å / Num. obs: 108281 / % possible obs: 90.2 % / Redundancy: 3.9 % / CC1/2: 0.997 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.054 / Rrim(I) all: 0.108 / Χ2: 0.89 / Net I/σ(I): 9.2 / Num. measured all: 422327
Reflection shellResolution: 1.49→1.51 Å / % possible obs: 86.6 % / Redundancy: 3.8 % / Rmerge(I) obs: 1.248 / Num. measured all: 19351 / Num. unique obs: 5120 / CC1/2: 0.674 / Rpim(I) all: 0.738 / Rrim(I) all: 1.451 / Χ2: 0.75 / Net I/σ(I) obs: 1.5

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.49→34.8 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 19.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1826 5406 5 %
Rwork0.1541 --
obs0.1556 108050 90 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.49→34.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5676 0 0 647 6323
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065803
X-RAY DIFFRACTIONf_angle_d0.9527864
X-RAY DIFFRACTIONf_dihedral_angle_d9.431824
X-RAY DIFFRACTIONf_chiral_restr0.083916
X-RAY DIFFRACTIONf_plane_restr0.007994
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.49-1.510.3131670.26063159X-RAY DIFFRACTION84
1.51-1.520.28461810.22473433X-RAY DIFFRACTION89
1.52-1.540.25071790.20623389X-RAY DIFFRACTION90
1.54-1.560.22511790.1893408X-RAY DIFFRACTION91
1.56-1.580.21861840.18273499X-RAY DIFFRACTION90
1.58-1.60.22841780.17663381X-RAY DIFFRACTION91
1.6-1.630.2251830.16863477X-RAY DIFFRACTION90
1.63-1.650.18911780.16383384X-RAY DIFFRACTION90
1.65-1.680.21421790.15653381X-RAY DIFFRACTION89
1.68-1.70.23391780.15123392X-RAY DIFFRACTION89
1.7-1.730.19671740.14233305X-RAY DIFFRACTION87
1.73-1.770.181710.14173241X-RAY DIFFRACTION85
1.77-1.80.18781550.14452950X-RAY DIFFRACTION78
1.8-1.840.19071840.14413476X-RAY DIFFRACTION91
1.84-1.880.18171840.14053526X-RAY DIFFRACTION93
1.88-1.920.17521890.13933588X-RAY DIFFRACTION93
1.92-1.970.19621830.14473452X-RAY DIFFRACTION92
1.97-2.020.16871870.14093564X-RAY DIFFRACTION93
2.02-2.080.17771840.13773470X-RAY DIFFRACTION93
2.08-2.150.17511850.14153528X-RAY DIFFRACTION92
2.15-2.220.16521830.14883463X-RAY DIFFRACTION91
2.22-2.310.18791800.14783421X-RAY DIFFRACTION90
2.31-2.420.18821760.15053361X-RAY DIFFRACTION89
2.42-2.550.17371570.15252980X-RAY DIFFRACTION79
2.55-2.710.18791900.16053606X-RAY DIFFRACTION95
2.71-2.910.18561920.16723640X-RAY DIFFRACTION95
2.91-3.210.21451920.17733660X-RAY DIFFRACTION96
3.21-3.670.17471890.16543580X-RAY DIFFRACTION94
3.67-4.620.15211780.1363390X-RAY DIFFRACTION89
4.62-34.80.13721870.13483540X-RAY DIFFRACTION93

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