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- PDB-1n92: Horse Liver Alcohol Dehydrogenase Complexed with NAD+ and 4-Iodop... -

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Basic information

Entry
Database: PDB / ID: 1n92
TitleHorse Liver Alcohol Dehydrogenase Complexed with NAD+ and 4-Iodopyrazole
ComponentsAlcohol Dehydrogenase E chain
KeywordsOXIDOREDUCTASE / dehydrogenase / alcohol / nicotinamide coenzyme / 4-iodopyrazole
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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE (ACIDIC FORM) / 4-IODOPYRAZOLE / Alcohol dehydrogenase E chain
Similarity search - Component
Biological speciesEquus caballus (horse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.47 Å
AuthorsRubach, J.K. / Plapp, B.V.
Citation
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.
#1: Journal: Biochemistry / Year: 1982
Title: Pyrazole Binding in Crystalline Binary and Ternary Complexes with Liver Alcohol Dehydrogenase
Authors: Eklund, H. / Samama, J.P. / Wallen, L.
#2: Journal: J.Biol.Chem. / Year: 1996
Title: X-Ray Structure of Human beta3beta3 Alcohol Dehydrogenase. The contribution of ionic interactions to coenzyme binding.
Authors: Davis, G.J. / Bosron, W.F. / Stone, C.L. / Owusu-Dekyi, K. / Hurley, T.D.
#3: Journal: J.Mol.Biol. / Year: 1994
Title: Structures of Three Human Beta Alcohol Dehydrogenase Variants. Correlations with their Functional Differences.
Authors: Hurley, T.D. / Bosron, W.F. / Stone, C.L. / Amzel, L.M.
#4: Journal: J.Mol.Biol. / Year: 1981
Title: Structure of A Triclinic Ternary Complex of Horse Liver Alcohol Dehydrogenase at 2.9 A Resolution
Authors: Eklund, H. / Samama, J.P. / Wallen, L. / Branden, C.I. / Akeson, A. / Jones, T.A.
#5: Journal: J.Mol.Biol. / Year: 1976
Title: Three-Dimensional Structure of Horse Liver Alcohol Dehydrogenase at 2.4 A Resolution
Authors: Eklund, H. / Nordstrom, B. / Zeppezauer, E. / Soderlund, G. / Ohlsson, I. / Boiwe, T. / Soderberg, B.O. / Tapia, O. / Branden, C.I. / Akeson, A.
History
DepositionNov 21, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 4, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_leaving_atom_flag / _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_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_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 600HETEROGEN THE STRUCTURE DETERMINED IN THIS ENTRY CONTAINS THE HETEROATOM MOLECULE NAJ, WHICH IS ...HETEROGEN THE STRUCTURE DETERMINED IN THIS ENTRY CONTAINS THE HETEROATOM MOLECULE NAJ, WHICH IS OXIDIZED NICOTINAMIDE ADENINE DINUCLEOTIDE, BUT THE RESTRAINTS ON THE PLANARITY OF THE NICOTINAMIDE RING WERE REMOVED DURING REFINEMENT WITH THE RESULT THAT THE RING IS PUCKERED. THE STRUCTURE ALSO INCLUDES 4-IODOPYRAZOLE, WHICH FORMS A PARTIAL COVALENT BOND BETWEEN N2 AND NC4 OF THE NICOTINAMIDE RING. NOTE THAT THE ABBREVIATION "PYZ" MEANS 4-IODOPYRAZOLE.
Remark 285CRYST1 TO GENERATE THE STANDARD UNIT CELL FOR P1 FROM THE CELL DESCRIBED IN THE CRYST CARD, APPLY ...CRYST1 TO GENERATE THE STANDARD UNIT CELL FOR P1 FROM THE CELL DESCRIBED IN THE CRYST CARD, APPLY THE FOLLOWING: 0.000000 1.000000 0.000000 0.00000 1.000000 0.000000 -1.000000 0.00000 -1.000000 0.000000 0.000000 0.00000 WHICH YIELDS THE FOLLOWING UNIT CELL PARAMETERS: 51.0 92.5 44.2 102.9 109.8 91.7 P 1

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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)81,80111
Polymers79,7072
Non-polymers2,0959
Water10,467581
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6990 Å2
ΔGint-118 kcal/mol
Surface area26620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.200, 51.050, 93.230
Angle α, β, γ (deg.)78.96, 75.47, 70.24
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, 590 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-PYZ / 4-IODOPYRAZOLE


Mass: 193.974 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H3IN2
#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.: 581 / 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: 2.17 Å3/Da / Density % sol: 42.89 %
Crystal growTemperature: 277 K / Method: dialysis / pH: 7 / Details: MPD, pH 7.0, Dialysis, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 6.7 / Method: microdialysis
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlenzyme11
250 mMammonium TES12
30.25 mMEDTA12pH6.7
41 mMNAD+12
51 mM4-iodopyrazole12
616 %MPD12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 28, 2001 / Details: confocal osmic
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.47→20 Å / Num. all: 156075 / Num. obs: 109109 / % possible obs: 88.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.1 % / Rmerge(I) obs: 0.054 / Rsym value: 0.054 / Net I/σ(I): 5.9
Reflection shellResolution: 1.47→1.508 Å / Rmerge(I) obs: 0.127 / Mean I/σ(I) obs: 4.1 / Num. unique all: 5097 / Rsym value: 0.127 / % possible all: 69
Reflection
*PLUS
Num. measured all: 227408
Reflection shell
*PLUS
% possible obs: 69 %

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Processing

Software
NameVersionClassification
d*TREKdata scaling
d*TREKdata reduction
AMoREphasing
REFMAC5.1.27refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HLD

1hld


Resolution: 1.47→20 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.961 / SU B: 1.121 / SU ML: 0.042 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.078 / ESU R Free: 0.068 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1831 2234 2 %RANDOM
Rwork0.151 ---
all0.1515 156075 --
obs0.151 109109 88.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 17.152 Å2
Baniso -1Baniso -2Baniso -3
1--0.25 Å2-0.02 Å20.78 Å2
2---0.21 Å20.04 Å2
3---0.06 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.068 Å0.042 Å
Refinement stepCycle: LAST / Resolution: 1.47→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5570 0 104 589 6263
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0225789
X-RAY DIFFRACTIONr_bond_other_d00.025360
X-RAY DIFFRACTIONr_angle_refined_deg1.6342.0137840
X-RAY DIFFRACTIONr_angle_other_deg3.6083.00112540
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0515746
X-RAY DIFFRACTIONr_chiral_restr0.1060.2913
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026302
X-RAY DIFFRACTIONr_gen_planes_other0.0080.021066
X-RAY DIFFRACTIONr_nbd_refined0.2330.21083
X-RAY DIFFRACTIONr_nbd_other0.2880.25845
X-RAY DIFFRACTIONr_nbtor_other0.1060.22643
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0940.2
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2170.27
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3080.222
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1120.28
X-RAY DIFFRACTIONr_mcbond_it1.5131.53704
X-RAY DIFFRACTIONr_mcangle_it2.27625990
X-RAY DIFFRACTIONr_scbond_it3.60432085
X-RAY DIFFRACTIONr_scangle_it5.2584.51850
X-RAY DIFFRACTIONr_rigid_bond_restr1.37625782
X-RAY DIFFRACTIONr_sphericity_free9.49624
X-RAY DIFFRACTIONr_sphericity_bonded7.94325670
LS refinement shellResolution: 1.47→1.508 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.45 93
Rwork0.373 5097
obs-5097
Refinement
*PLUS
Lowest resolution: 20 Å / % reflection Rfree: 2.5 % / Rfactor Rfree: 0.183
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.016
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.63

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