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- PDB-1lde: HORSE LIVER ALCOHOL DEHYDROGENASE COMPLEXED TO NADH AND N-FORMYL ... -

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Basic information

Entry
Database: PDB / ID: 1lde
TitleHORSE LIVER ALCOHOL DEHYDROGENASE COMPLEXED TO NADH AND N-FORMYL PIPERDINE
ComponentsLIVER ALCOHOL DEHYDROGENASE
KeywordsDEHYDROGENASE / ALCOHOL / NICOTINAMIDE COENZYME / FORMAMIDES / OXIDOREDUCTASE
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
N-FORMYLPIPERIDINE / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Alcohol dehydrogenase E chain
Similarity search - Component
Biological speciesEquus caballus (horse)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsRamaswamy, S. / Plapp, B.V.
Citation
Journal: Biochemistry / Year: 1997
Title: Binding of formamides to liver alcohol dehydrogenase.
Authors: Ramaswamy, S. / Scholze, M. / Plapp, B.V.
#1: 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.
#2: Journal: J.Biol.Chem. / Year: 1982
Title: Binding of Substrate in a Ternary Complex of Horse Liver Alcohol Dehydrogenase
Authors: Eklund, H. / Plapp, B.V. / Samama, J.P. / Branden, C.I.
#3: 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. / Samma, J.P. / Wallen, L. / Branden, C.I. / Akeson, A. / Jones, T.A.
#4: 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
DepositionDec 25, 1996Processing site: BNL
Revision 1.0Apr 1, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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.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_conn.ptnr2_label_seq_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: LIVER ALCOHOL DEHYDROGENASE
B: LIVER ALCOHOL DEHYDROGENASE
C: LIVER ALCOHOL DEHYDROGENASE
D: LIVER ALCOHOL DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,04320
Polymers159,4134
Non-polymers3,63016
Water10,016556
1
B: LIVER ALCOHOL DEHYDROGENASE
hetero molecules

C: LIVER ALCOHOL DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,52110
Polymers79,7072
Non-polymers1,8158
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_565x,y+1,z1
Buried area6850 Å2
ΔGint-109 kcal/mol
Surface area26170 Å2
MethodPISA
2
A: LIVER ALCOHOL DEHYDROGENASE
D: LIVER ALCOHOL DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,52110
Polymers79,7072
Non-polymers1,8158
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6840 Å2
ΔGint-108 kcal/mol
Surface area26230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.930, 180.200, 86.800
Angle α, β, γ (deg.)90.00, 106.00, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.9968, -0.00862, 0.07936), (0.00991, 0.9998, -0.01588), (-0.07921, 0.01661, 0.9967)-15.75, -179.60001, -41.94
2given(0.07432, -0.09822, 0.9924), (-0.1213, -0.9886, -0.08876), (0.9898, -0.1138, -0.08538)-36.08, 49.46, -11.2
3given(0.1693, -0.107, 0.9797), (-0.1107, -0.9899, -0.08898), (0.9793, -0.09334, -0.1794)4.386, 44.07, -0.5444

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Components

#1: Protein
LIVER ALCOHOL DEHYDROGENASE / ADH


Mass: 39853.273 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Details: COMMERCIAL PREPARATION OF ENZYME FROM HORSE LIVER. CDNA SEQUENCE M64864
Source: (natural) Equus caballus (horse) / Cellular location: CYTOPLASM / Organ: LIVER / References: UniProt: P00327, alcohol dehydrogenase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Chemical
ChemComp-FPI / N-FORMYLPIPERIDINE


Mass: 113.158 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H11NO
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 556 / 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: 2.35 Å3/Da / Density % sol: 47 % / Description: ISOMORPHOUS STRUCTURE WAS USED
Crystal growMethod: batch dialysis / pH: 7
Details: PROTEIN WAS CRYSTALLIZED BY THE BATCH DIALYSIS METHOD USING MPD AS THE PRECIPITANT AT PH 7.0, 50 MM AMMONIUM N-[TRIS(HYDROXYMETHYL)METHYL]-2 AMINOETHANESULFONATE, WITH 0.66 MM NADH AND 0.76 ...Details: PROTEIN WAS CRYSTALLIZED BY THE BATCH DIALYSIS METHOD USING MPD AS THE PRECIPITANT AT PH 7.0, 50 MM AMMONIUM N-[TRIS(HYDROXYMETHYL)METHYL]-2 AMINOETHANESULFONATE, WITH 0.66 MM NADH AND 0.76 MM 3-BUTYLTHIOLANE 1-OXIDE. VERY CLOSE TO C-CENTERED ORTHORHOMBIC BUT SCALES VERY BADLY AS C222. SO THE SYMMETRY IS ACTUALLY P21., batch dialysis
Crystal grow
*PLUS
Temperature: 5 ℃ / Method: microdialysis
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlalcohol dehydrogenase1drop
250 mMammonium N-[tris(hydroxymethyl)methyl]-2-aminoethanesulfonate1reservoir
30.66 mMNADH1reservoir
414 mMN-formylpiperidine1reservoir
525 %MPD1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Apr 1, 1995 / Details: MIRRORS
RadiationMonochromator: NI / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. obs: 94632 / % possible obs: 88.8 % / Redundancy: 2.1 % / Rsym value: 0.035 / Net I/σ(I): 18.8
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 1.7 % / Mean I/σ(I) obs: 8.8 / Rsym value: 0.087 / % possible all: 77.2
Reflection
*PLUS
Rmerge(I) obs: 0.035
Reflection shell
*PLUS
% possible obs: 77.2 % / Rmerge(I) obs: 0.087

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Processing

Software
NameClassification
ARP/wARPmodel building
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.5→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
Details: THE STRUCTURE WAS REFINED THROUG OUT WITH LARGE NCS RESTRAINTS. WATER WAS ADDED AUTOMATICALLY BY THE PROGRAM ARP.
RfactorNum. reflection% reflectionSelection details
Rfree0.256 1379 3 %RANDOM
Rwork0.205 ---
obs-44760 88.8 %-
Displacement parametersBiso mean: 18.51 Å2
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11140 0 216 556 11912
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.030.02
X-RAY DIFFRACTIONp_angle_d0.060.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.060.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.762
X-RAY DIFFRACTIONp_mcangle_it2.553
X-RAY DIFFRACTIONp_scbond_it2.782
X-RAY DIFFRACTIONp_scangle_it4.23
X-RAY DIFFRACTIONp_plane_restr0.01
X-RAY DIFFRACTIONp_chiral_restr0.20.15
X-RAY DIFFRACTIONp_singtor_nbd0.1930.3
X-RAY DIFFRACTIONp_multtor_nbd0.270.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor2.37
X-RAY DIFFRACTIONp_staggered_tor15.815
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor33.520
X-RAY DIFFRACTIONp_special_tor015
Software
*PLUS
Name: 'REFMAC' / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.205
Solvent computation
*PLUS
Displacement parameters
*PLUS

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