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- PDB-7jqa: EQADH-NADH-4-BROMOBENZYL ALCOHOL, P21 -

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Basic information

Entry
Database: PDB / ID: 7jqa
TitleEQADH-NADH-4-BROMOBENZYL ALCOHOL, P21
ComponentsAlcohol dehydrogenase E chain
KeywordsOXIDOREDUCTASE / alcohol dehydrogenase / NADH / horse liver
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 Rossmann-like Domain ...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 Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PARA-BROMOBENZYL ALCOHOL / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / Alcohol dehydrogenase E chain
Similarity search - Component
Biological speciesEquus caballus (horse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.53 Å
AuthorsPlapp, B.V. / Ramaswamy, S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Alcohol Abuse and Alcoholism (NIH/NIAAA)AA00279 United States
Citation
Journal: Arch.Biochem.Biophys. / Year: 2021
Title: Alternative binding modes in abortive NADH-alcohol complexes of horse liver alcohol dehydrogenase.
Authors: Plapp, B.V. / Subramanian, R.
#1: Journal: Biochemistry / Year: 2012
Title: Atomic-resolution structures of horse liver alcohol dehydrogenase with NAD(+) and fluoroalcohols define strained Michaelis complexes.
Authors: Plapp, B.V. / Ramaswamy, S.
#2: Journal: Biochemistry / Year: 2017
Title: Horse Liver Alcohol Dehydrogenase: Zinc Coordination and Catalysis.
Authors: Plapp, B.V. / Savarimuthu, B.R. / Ferraro, D.J. / Rubach, J.K. / Brown, E.N. / Ramaswamy, S.
#3: Journal: Biochemistry / Year: 1994
Title: Structures of horse liver alcohol dehydrogenase complexed with NAD+ and substituted benzyl alcohols.
Authors: Ramaswamy, S. / Eklund, H. / Plapp, B.V.
History
DepositionAug 10, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 17, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
C: Alcohol dehydrogenase E chain
D: Alcohol dehydrogenase E chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,46421
Polymers159,4134
Non-polymers4,05117
Water18,6281034
1
A: Alcohol dehydrogenase E chain
B: Alcohol dehydrogenase E chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,67310
Polymers79,7072
Non-polymers1,9678
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7030 Å2
ΔGint-113 kcal/mol
Surface area26450 Å2
MethodPISA
2
C: Alcohol dehydrogenase E chain
D: Alcohol dehydrogenase E chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,79111
Polymers79,7072
Non-polymers2,0859
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7180 Å2
ΔGint-118 kcal/mol
Surface area26520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.050, 180.140, 86.660
Angle α, β, γ (deg.)90.000, 105.960, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Alcohol dehydrogenase E chain


Mass: 39853.273 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Equus caballus (horse) / References: UniProt: P00327, alcohol dehydrogenase

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Non-polymers , 5 types, 1051 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH


Mass: 665.441 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H29N7O14P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-BRB / PARA-BROMOBENZYL ALCOHOL


Mass: 187.034 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C7H7BrO / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1034 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.23 Å3/Da / Density % sol: 45 % / Description: block
Crystal growTemperature: 278 K / Method: microdialysis / pH: 7
Details: 50 MM AMMONIUM-N-[TRIS(HYDROXYMETHYL) - METHYL]-2-AMINOETHANE SULFONATE, PH 6.7 (AT 25 C), 0.25 MM EDTA, 10 MG/ML PROTEIN, 1 MM NAD+, 10 MM 4-bromobenzyl alcohol, 12 TO 25 % 2-METHYL-2,4-PENTANEDIOL

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Apr 23, 2004 / Details: confocal
RadiationMonochromator: grafite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.53→19.91 Å / Num. obs: 170706 / % possible obs: 77.2 % / Redundancy: 5.31 % / Rmerge(I) obs: 0.063 / Rrim(I) all: 0.068 / Χ2: 1.13 / Net I/σ(I): 15.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRrim(I) allΧ2Rejects% possible all
1.53-1.582.260.3222.729531130550.4070.941059.2
1.58-1.652.490.287336770147410.3590.9466.8
1.65-1.722.960.2663.546075155770.3220.9370.6
1.72-1.813.70.2294.561104164970.2671.011274.9
1.81-1.934.660.1956.182435176720.221.110879.8
1.93-2.086.380.1598116817182620.1721.0923882.8
2.08-2.286.50.12210.3114666176060.1321.0621779.8
2.28-2.616.750.09713.7115401170250.1051.0740377.1
2.61-3.297.150.06921.7132492183850.0741.1798783.2
3.29-19.97.950.04236.4178827218860.0461.37487798.2

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Processing

Software
NameVersionClassification
d*TREK9.9.9.8Ldata scaling
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
d*TREKdata reduction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5vl0

5vl0


Resolution: 1.53→19.91 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.958 / SU B: 4.464 / SU ML: 0.068 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.116 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2207 1693 1 %RANDOM
Rwork0.1481 ---
obs0.1488 168958 77.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 89.33 Å2 / Biso mean: 21.449 Å2 / Biso min: 11.21 Å2
Baniso -1Baniso -2Baniso -3
1-1.72 Å2-0 Å2-0.8 Å2
2---0.6 Å20 Å2
3----0.56 Å2
Refinement stepCycle: final / Resolution: 1.53→19.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11140 0 228 1039 12407
Biso mean--20.29 30.88 -
Num. residues----1496
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.01311655
X-RAY DIFFRACTIONr_bond_other_d0.0010.01711184
X-RAY DIFFRACTIONr_angle_refined_deg1.8951.68115794
X-RAY DIFFRACTIONr_angle_other_deg1.471.59126059
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8951500
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.78522.883444
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.342152024
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2151548
X-RAY DIFFRACTIONr_chiral_restr0.0940.21582
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212750
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022218
X-RAY DIFFRACTIONr_rigid_bond_restr3.183322839
LS refinement shellResolution: 1.53→1.57 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.369 72 -
Rwork0.292 9148 -
all-9220 -
obs--56.59 %

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