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- PDB-4dwv: Horse alcohol dehydrogenase complexed with NAD+ and 2,3,4,5,6-pen... -

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Basic information

Entry
Database: PDB / ID: 4dwv
TitleHorse alcohol dehydrogenase complexed with NAD+ and 2,3,4,5,6-pentafluorobenzyl alcohol
ComponentsAlcohol dehydrogenase E chain
KeywordsOXIDOREDUCTASE / ALCOHOL DEHYDROGENASE / NAD+ / PENTAFLUOROBENZYL ALCOHOL / MICHAELIS COMPLEX / ROSSMANN FOLD
Function / homology
Function and homology information


all-trans-retinol dehydrogenase (NAD+) activity / alcohol dehydrogenase / alcohol dehydrogenase (NAD+) activity / 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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE (ACIDIC FORM) / 2,3,4,5,6-PENTAFLUOROBENZYL ALCOHOL / Alcohol dehydrogenase E chain
Similarity search - Component
Biological speciesEquus caballus (horse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.14 Å
AuthorsPlapp, B.V. / Ramaswamy, S.
Citation
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.
#1: 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.
#2: Journal: Biochemistry / Year: 2003
Title: Amino acid residues in the nicotinamide binding site contribute to catalysis by horse liver alcohol dehydrogenase.
Authors: Rubach, J.K. / Plapp, B.V.
#3: 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.
History
DepositionFeb 26, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 11, 2012Provider: repository / Type: Initial release
Revision 1.1May 16, 2012Group: Database references
Revision 1.2Jun 27, 2012Group: Database references
Revision 1.3Feb 12, 2020Group: Database references / Category: pdbx_related_exp_data_set
Revision 1.4Sep 13, 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,16414
Polymers79,7072
Non-polymers2,45712
Water18,7361040
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7730 Å2
ΔGint-106 kcal/mol
Surface area26650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.290, 51.440, 92.490
Angle α, β, γ (deg.)91.72, 103.09, 110.11
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Alcohol dehydrogenase E chain


Mass: 39853.273 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Equus caballus (horse) / Organ: liver / References: UniProt: P00327, alcohol dehydrogenase

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Non-polymers , 5 types, 1052 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-NAJ / NICOTINAMIDE-ADENINE-DINUCLEOTIDE (ACIDIC FORM)


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2
#4: Chemical ChemComp-PFB / 2,3,4,5,6-PENTAFLUOROBENZYL ALCOHOL


Mass: 198.090 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H3F5O
#5: Chemical
ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1040 / 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: 2.4 Å3/Da / Density % sol: 48.77 %
Crystal growTemperature: 278 K / Method: microdialysis / pH: 6.7
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 2,3,4,5,6-pentafluorobenzyl alcohol, 12 to 25 % 2- ...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 2,3,4,5,6-pentafluorobenzyl alcohol, 12 to 25 % 2-methyl-2,4-pentanediol, MICRODIALYSIS, temperature 278k

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.9537 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 9, 2006 / Details: ADJUSTABLE FOCUS K-B PAIR SI PLUS PT, RH COATINGS
RadiationMonochromator: DOUBLE CRYSTAL CRYOCOOLED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.14→20 Å / Num. all: 270489 / Num. obs: 253394 / % possible obs: 93.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.75 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 12.9
Reflection shellResolution: 1.14→1.18 Å / Redundancy: 3.74 % / Rmerge(I) obs: 0.264 / Mean I/σ(I) obs: 3.2 / % possible all: 84.5

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
AMoREphasing
REFMAC5.5.0102refinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1HLD

1hld


Resolution: 1.14→20 Å / Cor.coef. Fo:Fc: 0.985 / Cor.coef. Fo:Fc free: 0.983 / SU B: 0.961 / SU ML: 0.02 / Cross valid method: THROUGHOUT / ESU R: 0.028 / ESU R Free: 0.028 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.14373 2572 1 %RANDOM
Rwork0.12387 ---
obs0.12406 250826 93.65 %-
all-270489 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.926 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å2-0.5 Å20.21 Å2
2--0.26 Å2-0.06 Å2
3----0.63 Å2
Refinement stepCycle: LAST / Resolution: 1.14→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5570 0 150 1040 6760
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.026044
X-RAY DIFFRACTIONr_bond_other_d0.0020.024130
X-RAY DIFFRACTIONr_angle_refined_deg1.6732.0278209
X-RAY DIFFRACTIONr_angle_other_deg1.0033.00210254
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.245762
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.25624.739211
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.32151107
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.8831524
X-RAY DIFFRACTIONr_chiral_restr0.1020.2974
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0216459
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021081
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_it1.4791.53779
X-RAY DIFFRACTIONr_mcbond_other0.5211.51544
X-RAY DIFFRACTIONr_mcangle_it2.19126172
X-RAY DIFFRACTIONr_scbond_it3.16832265
X-RAY DIFFRACTIONr_scangle_it4.7344.52030
X-RAY DIFFRACTIONr_rigid_bond_restr3.422310174
X-RAY DIFFRACTIONr_sphericity_free31.71610220
X-RAY DIFFRACTIONr_sphericity_bonded9.4391010906
LS refinement shellResolution: 1.14→1.17 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 177 -
Rwork0.266 16277 -
obs--82.2 %

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