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- PDB-1ldy: HORSE LIVER ALCOHOL DEHYDROGENASE COMPLEXED TO NADH AND CYCLOHEXY... -

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Basic information

Entry
Database: PDB / ID: 1ldy
TitleHORSE LIVER ALCOHOL DEHYDROGENASE COMPLEXED TO NADH AND CYCLOHEXYL FORMAMIDE (CXF)
ComponentsALCOHOL DEHYDROGENASE
KeywordsDEHYDROGENASE / ALCOHOL / NICOTINAMIDE COENZYME / FORMAMIDES
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
CYCLOHEXYLFORMAMIDE / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Alcohol dehydrogenase E chain
Similarity search - Component
Biological speciesEquus caballus (horse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / 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. / Samama, 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 23, 1996Processing site: BNL
Revision 1.0Apr 21, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_database_status / 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 / _diffrn_source.pdbx_synchrotron_site / _pdbx_database_status.process_site / _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: ALCOHOL DEHYDROGENASE
B: ALCOHOL DEHYDROGENASE
C: ALCOHOL DEHYDROGENASE
D: ALCOHOL DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,09920
Polymers159,4134
Non-polymers3,68616
Water18,2311012
1
A: ALCOHOL DEHYDROGENASE
D: ALCOHOL DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,54910
Polymers79,7072
Non-polymers1,8438
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6980 Å2
ΔGint-105 kcal/mol
Surface area26260 Å2
MethodPISA
2
B: ALCOHOL DEHYDROGENASE
C: ALCOHOL DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,54910
Polymers79,7072
Non-polymers1,8438
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7000 Å2
ΔGint-106 kcal/mol
Surface area26260 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(0.998981, -0.006279, 0.044696), (0.006694, 0.999936, -0.009129), (-0.044636, 0.009418, 0.998959)-15.54077, 0.29212, -40.15073
2given(0.079823, -0.098401, 0.99194), (-0.116883, -0.989175, -0.088721), (0.989933, -0.108858, -0.09046)-36.15647, 49.33366, -11.10387
3given(0.136862, -0.100503, 0.985479), (-0.108357, -0.990389, -0.085955), (0.984646, -0.09502, -0.146436)4.8495, 43.95399, -1.25633

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Components

#1: Protein
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-CXF / CYCLOHEXYLFORMAMIDE


Mass: 127.184 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C7H13NO
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1012 / 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 NUMBER OF TOTAL REFLECTIONS : 122542
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 dehydrogenase11
250 mMammonium N-[tris(hydroxymethyl)methyl]-2-aminoethanesulfonate12
30.66 mMNADH12
410 mMN-cyclohexylformamide12
525 %MPD12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 0.99
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 1, 1996
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 2.5→12 Å / % possible obs: 92.9 % / Redundancy: 2.6 % / Biso Wilson estimate: 28 Å2 / Rsym value: 0.042 / Net I/σ(I): 21.86
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 12 / Rsym value: 0.059 / % possible all: 81.8
Reflection
*PLUS
Num. obs: 46126 / Rmerge(I) obs: 0.042
Reflection shell
*PLUS
Mean I/σ(I) obs: 12.8

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.5→12 Å / Cross valid method: UNTIL ANISOTROPIC REFINEMENT / σ(F): 0
Details: THE STRUCTURE WAS REFINED THROUGHOUT WITH LARGE NCS RESTRAINTS. WATER WAS ADDED ONLY WHEN FOUND IN ALL FOUR SUBUNITS. THE CYS 174 AND ITS EQUIVALENT LIE IN THE DISALLOWED REGION OF ...Details: THE STRUCTURE WAS REFINED THROUGHOUT WITH LARGE NCS RESTRAINTS. WATER WAS ADDED ONLY WHEN FOUND IN ALL FOUR SUBUNITS. THE CYS 174 AND ITS EQUIVALENT LIE IN THE DISALLOWED REGION OF RAMACHANDRAN PLOT - THIS IS TRUE IN SEVERAL STRUCTURES OF ADH REFINED WITH SEVERAL COMPLEXES AND IS A FEATURE OF THE ENZYME.
RfactorNum. reflection% reflectionSelection details
Rwork0.207 ---
obs-46126 89.8 %-
Rfree---RANDOM
Displacement parametersBiso mean: 27.6 Å2
Baniso -1Baniso -2Baniso -3
1--9.53 Å20 Å2-2.49 Å2
2--10.9 Å20 Å2
3----1.37 Å2
Refinement stepCycle: LAST / Resolution: 2.5→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11140 0 220 1012 12372
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.020.02
X-RAY DIFFRACTIONp_angle_d0.050.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.050.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.112
X-RAY DIFFRACTIONp_mcangle_it1.673
X-RAY DIFFRACTIONp_scbond_it1.462
X-RAY DIFFRACTIONp_scangle_it2.253
X-RAY DIFFRACTIONp_plane_restr0.01
X-RAY DIFFRACTIONp_chiral_restr0.1490.15
X-RAY DIFFRACTIONp_singtor_nbd0.1890.3
X-RAY DIFFRACTIONp_multtor_nbd0.2590.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor1.67
X-RAY DIFFRACTIONp_staggered_tor17.815
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor34.420
X-RAY DIFFRACTIONp_special_tor015
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.207
Solvent computation
*PLUS
Displacement parameters
*PLUS

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