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- PDB-5vn1: horse liver alcohol dehydrogenae complexed with NADH (R,S)-N-1-me... -

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Basic information

Entry
Database: PDB / ID: 5vn1
Titlehorse liver alcohol dehydrogenae complexed with NADH (R,S)-N-1-methylhexylformamide
ComponentsAlcohol dehydrogenase E chain
KeywordsOXIDOREDUCTASE / alcohol dehydrogenase / horse liver / NADH N-1-methylhexylformamide
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. / Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / Polyketide synthase, enoylreductase domain / Enoylreductase ...Alcohol dehydrogenase, zinc-type, conserved site / Zinc-containing alcohol dehydrogenases signature. / Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / 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 / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / (R)-N-(1-METHYL-HEXYL)-FORMAMIDE / N-[(2S)-heptan-2-yl]formamide / Alcohol dehydrogenase E chain
Similarity search - Component
Biological speciesEquus caballus (horse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsPlapp, B.V. / Ramaswamy, S. / Ferraro, D.J. / Baskar Raj, S.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Alcohol Abuse and Alcoholism (NIH/NIAAA)AA00279 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32 GM08365 United States
Citation
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.
#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: J. Biol. Chem. / Year: 2003
Title: Formamides mimic aldehydes and inhibit liver alcohol dehydrogenases and ethanol metabolism.
Authors: Venkataramaiah, T.H. / Plapp, B.V.
#3: Journal: Biochemistry / Year: 1997
Title: Flexibility of liver alcohol dehydrogenase in stereoselective binding of 3-butylthiolane 1-oxides.
Authors: Cho, H. / Ramaswamy, S. / Plapp, B.V.
#4: Journal: Biochemistry / Year: 1997
Title: Binding of formamides to liver alcohol dehydrogenase.
Authors: Ramaswamy, S. / Scholze, M. / Plapp, B.V.
History
DepositionApr 28, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 10, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 5, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Aug 2, 2017Group: Author supporting evidence / Database references / Category: citation / pdbx_audit_support
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _pdbx_audit_support.funding_organization
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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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)163,55123
Polymers159,4134
Non-polymers4,13819
Water23,7981321
1
A: Alcohol dehydrogenase E chain
B: Alcohol dehydrogenase E chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,70411
Polymers79,7072
Non-polymers1,9979
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6050 Å2
ΔGint-57 kcal/mol
Surface area27240 Å2
MethodPISA
2
C: Alcohol dehydrogenase E chain
D: Alcohol dehydrogenase E chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,84712
Polymers79,7072
Non-polymers2,14010
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6340 Å2
ΔGint-57 kcal/mol
Surface area26890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.212, 180.808, 86.841
Angle α, β, γ (deg.)90.000, 106.120, 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 , 6 types, 1340 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
#4: Chemical
ChemComp-NWH / N-[(2S)-heptan-2-yl]formamide / (S)-N-1-methylhexylformamide


Mass: 143.227 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H17NO
#5: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Chemical ChemComp-NMH / (R)-N-(1-METHYL-HEXYL)-FORMAMIDE


Mass: 143.227 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H17NO
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1321 / Source method: isolated from a natural source / Formula: H2O

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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: 2.38 Å3/Da / Density % sol: 48.22 % / Description: long block
Crystal growTemperature: 278 K / Method: microdialysis / pH: 7
Details: 10 mg protein/ml dialyzed against 50 mM ammonium N-[tris(hydroxymethyl)methyl]-2-aminoethanesulfonate buffer, pH 7 (pH 6.7 at 25 deg C) with 1 mM NADH and 10 mM (racemic) (R,S)-N-1- ...Details: 10 mg protein/ml dialyzed against 50 mM ammonium N-[tris(hydroxymethyl)methyl]-2-aminoethanesulfonate buffer, pH 7 (pH 6.7 at 25 deg C) with 1 mM NADH and 10 mM (racemic) (R,S)-N-1-methylhexylformamide as the concentration of 2-methyl-2,4-pentanediol was raised to 25%. Crystal on loop plunged into liquid N2.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.936 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Mar 1, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.936 Å / Relative weight: 1
ReflectionResolution: 1.2→20 Å / Num. obs: 386016 / % possible obs: 83.8 % / Observed criterion σ(I): -3 / Redundancy: 1.762 % / Rmerge F obs: 0.13 / Rmerge(I) obs: 0.122 / Rrim(I) all: 0.151 / Net I/σ(I): 5.77 / Num. measured all: 680160 / Scaling rejects: 57
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRrim(I) all% possible all
1.2-1.251.5180.3182.2357530.42667.5
1.25-1.31.5730.2541.98357780.33879.1
1.3-3.71.7160.1216.482996230.15486.4
3.7-3.83.6610.1388.9112040.16695.6
3.8-3.93.5930.1468.5610340.17795.7
3.9-43.650.1458.69350.17696
4-53.6810.1219.558140.14794.7
5-93.9010.0999.2549730.11893.2
9-103.4420.079.992740.08887
10-113.5210.099.711630.11283.2
11-203.5640.0738.894240.09382.8

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Processing

Software
NameVersionClassification
XSCALEdata scaling
REFMAC5.8.0158refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
X-PLORphasing
Omodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1p1r

1p1r


Resolution: 1.25→20 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.969 / SU B: 1.431 / SU ML: 0.027 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.05 / ESU R Free: 0.05
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1866 1650 0.5 %RANDOM
Rwork0.1515 ---
obs0.1517 325043 80.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 85.95 Å2 / Biso mean: 25.461 Å2 / Biso min: 15.64 Å2
Baniso -1Baniso -2Baniso -3
1-1.71 Å20 Å20.28 Å2
2---1.4 Å20 Å2
3----0.41 Å2
Refinement stepCycle: final / Resolution: 1.25→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11140 0 250 1329 12719
Biso mean--25.88 37.04 -
Num. residues----1496
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0211656
X-RAY DIFFRACTIONr_bond_other_d0.0020.0211268
X-RAY DIFFRACTIONr_angle_refined_deg1.8852.01115778
X-RAY DIFFRACTIONr_angle_other_deg1.063326239
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.27651496
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.37224.388392
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.536152021
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3121548
X-RAY DIFFRACTIONr_chiral_restr0.1220.21849
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02112620
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022162
X-RAY DIFFRACTIONr_rigid_bond_restr2.976322924
X-RAY DIFFRACTIONr_sphericity_free18.98410958
X-RAY DIFFRACTIONr_sphericity_bonded7.4181023084
LS refinement shellResolution: 1.25→1.282 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.229 122 -
Rwork0.197 21727 -
all-21849 -
obs--72.69 %

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