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- PDB-9cqk: Horse liver alcohol dehydrogenase F93W in complex with NADH and N... -

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Basic information

Entry
Database: PDB / ID: 9cqk
TitleHorse liver alcohol dehydrogenase F93W 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: 1.65 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 19, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 23, 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)82,00210
Polymers80,1552
Non-polymers1,8478
Water9,962553
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6820 Å2
ΔGint-106 kcal/mol
Surface area26360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.573, 45.448, 92.145
Angle α, β, γ (deg.)75.85, 78.69, 77.26
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Alcohol dehydrogenase E chain


Mass: 40077.488 Da / Num. of mol.: 2 / Mutation: F93W
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.: 553 / 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: 2.08 Å3/Da / Density % sol: 40.86 %
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 21, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.65→36.03 Å / Num. obs: 69665 / % possible obs: 89.4 % / Redundancy: 3.8 % / CC1/2: 0.985 / Rmerge(I) obs: 0.127 / Rpim(I) all: 0.076 / Rrim(I) all: 0.148 / Χ2: 1.02 / Net I/σ(I): 7 / Num. measured all: 261386
Reflection shellResolution: 1.65→1.68 Å / % possible obs: 85 % / Redundancy: 3.5 % / Rmerge(I) obs: 1.06 / Num. measured all: 11579 / Num. unique obs: 3318 / CC1/2: 0.553 / Rpim(I) all: 0.65 / Rrim(I) all: 1.246 / Χ2: 0.86 / Net I/σ(I) obs: 1.3

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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: 1.65→36.03 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 21.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2086 3463 5.02 %
Rwork0.1964 --
obs0.197 68997 88.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.65→36.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5576 0 110 553 6239
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0295814
X-RAY DIFFRACTIONf_angle_d1.8477881
X-RAY DIFFRACTIONf_dihedral_angle_d8.769824
X-RAY DIFFRACTIONf_chiral_restr0.139917
X-RAY DIFFRACTIONf_plane_restr0.01993
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.670.31241410.33752573X-RAY DIFFRACTION86
1.67-1.70.24661190.27642596X-RAY DIFFRACTION88
1.7-1.720.32011320.26742560X-RAY DIFFRACTION86
1.72-1.750.24651340.25552472X-RAY DIFFRACTION85
1.75-1.780.26421460.24622412X-RAY DIFFRACTION81
1.78-1.810.26031190.22662366X-RAY DIFFRACTION81
1.81-1.840.2221570.21332739X-RAY DIFFRACTION93
1.84-1.880.24881420.21782710X-RAY DIFFRACTION93
1.88-1.910.27881250.24952657X-RAY DIFFRACTION89
1.91-1.960.29361450.28232548X-RAY DIFFRACTION87
1.96-20.21981510.19792720X-RAY DIFFRACTION93
2-2.050.20851380.19242756X-RAY DIFFRACTION92
2.05-2.110.25761340.24342531X-RAY DIFFRACTION87
2.11-2.170.21521410.18392706X-RAY DIFFRACTION91
2.17-2.240.21251490.19182643X-RAY DIFFRACTION90
2.24-2.320.20771230.21482497X-RAY DIFFRACTION85
2.32-2.410.19141370.17672583X-RAY DIFFRACTION87
2.41-2.520.19781110.18382331X-RAY DIFFRACTION78
2.52-2.650.21971490.1872676X-RAY DIFFRACTION91
2.65-2.820.19221500.19192797X-RAY DIFFRACTION95
2.82-3.040.18391490.18042831X-RAY DIFFRACTION95
3.04-3.340.19021450.17632754X-RAY DIFFRACTION94
3.34-3.830.20331470.16852746X-RAY DIFFRACTION92
3.83-4.820.15671320.1582471X-RAY DIFFRACTION84
4.82-36.030.17141470.1752859X-RAY DIFFRACTION96
Refinement TLS params.Method: refined / Origin x: -17.8761 Å / Origin y: -13.2794 Å / Origin z: 19.8368 Å
111213212223313233
T0.086 Å20.0041 Å20.0058 Å2-0.1098 Å2-0.001 Å2--0.1205 Å2
L0.0874 °20.0263 °2-0.0083 °2-0.0685 °2-0.0371 °2--0.7192 °2
S-0.0092 Å °-0.0093 Å °0.0037 Å °0.0039 Å °0.0044 Å °0.0053 Å °0.0046 Å °-0.0568 Å °0.0054 Å °
Refinement TLS groupSelection details: all

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