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- PDB-5l2m: Structure of ALDH1A1 in complex with BUC11 -

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Basic information

Entry
Database: PDB / ID: 5l2m
TitleStructure of ALDH1A1 in complex with BUC11
ComponentsRetinal dehydrogenase 1
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INIHBITOR / ALDH1A1 Inhibitor / OXIDOREDUCTASE-OXIDOREDUCTASE INIHBITOR complex
Function / homology
Function and homology information


fructosamine catabolic process / 3-deoxyglucosone dehydrogenase activity / benzaldehyde dehydrogenase (NAD+) / acetaldehyde dehydrogenase (NAD+) activity / retinal dehydrogenase / benzaldehyde dehydrogenase (NAD+) activity / aminobutyraldehyde dehydrogenase / gamma-aminobutyric acid biosynthetic process / aminobutyraldehyde dehydrogenase (NAD+) activity / maintenance of lens transparency ...fructosamine catabolic process / 3-deoxyglucosone dehydrogenase activity / benzaldehyde dehydrogenase (NAD+) / acetaldehyde dehydrogenase (NAD+) activity / retinal dehydrogenase / benzaldehyde dehydrogenase (NAD+) activity / aminobutyraldehyde dehydrogenase / gamma-aminobutyric acid biosynthetic process / aminobutyraldehyde dehydrogenase (NAD+) activity / maintenance of lens transparency / Fructose catabolism / aldehyde metabolic process / Ethanol oxidation / RA biosynthesis pathway / aldehyde dehydrogenase (NAD+) / androgen binding / cellular detoxification of aldehyde / aldehyde dehydrogenase (NAD+) activity / retinal dehydrogenase (NAD+) activity / retinol metabolic process / negative regulation of cold-induced thermogenesis / retinoid metabolic process / GTPase activator activity / NAD binding / axon / synapse / extracellular exosome / cytosol / cytoplasm
Similarity search - Function
Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde dehydrogenase, glutamic acid active site / Aldehyde dehydrogenases glutamic acid active site. / Aldehyde dehydrogenase, cysteine active site / Aldehyde dehydrogenases cysteine active site. / Aldehyde dehydrogenase domain / Aldehyde dehydrogenase family ...Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde dehydrogenase, glutamic acid active site / Aldehyde dehydrogenases glutamic acid active site. / Aldehyde dehydrogenase, cysteine active site / Aldehyde dehydrogenases cysteine active site. / Aldehyde dehydrogenase domain / Aldehyde dehydrogenase family / Aldehyde dehydrogenase, C-terminal / Aldehyde dehydrogenase, N-terminal / Aldehyde/histidinol dehydrogenase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-6ZY / YTTERBIUM (III) ION / Aldehyde dehydrogenase 1A1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.7 Å
AuthorsBuchman, C.D. / Hurley, T.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R21 CA198409 United States
CitationJournal: J. Med. Chem. / Year: 2017
Title: Inhibition of the Aldehyde Dehydrogenase 1/2 Family by Psoralen and Coumarin Derivatives.
Authors: Buchman, C.D. / Hurley, T.D.
History
DepositionAug 2, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 8, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 5, 2017Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn
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_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Retinal dehydrogenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,5174
Polymers54,9411
Non-polymers5763
Water5,567309
1
A: Retinal dehydrogenase 1
hetero molecules

A: Retinal dehydrogenase 1
hetero molecules

A: Retinal dehydrogenase 1
hetero molecules

A: Retinal dehydrogenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)222,06616
Polymers219,7624
Non-polymers2,30412
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation5_655-x+1,y,-z1
crystal symmetry operation6_555x,-y,-z1
Buried area21640 Å2
ΔGint-137 kcal/mol
Surface area59640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.064, 109.064, 83.178
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number89
Space group name H-MP422
Components on special symmetry positions
IDModelComponents
11A-992-

HOH

21A-1001-

HOH

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Components

#1: Protein Retinal dehydrogenase 1 / RalDH1 / ALDH-E1 / ALHDII / Aldehyde dehydrogenase family 1 member A1 / Aldehyde dehydrogenase / cytosolic


Mass: 54940.617 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ALDH1A1, ALDC, ALDH1, PUMB1 / Production host: Escherichia coli (E. coli)
References: UniProt: P00352, Oxidoreductases; Acting on the aldehyde or oxo group of donors; With NAD+ or NADP+ as acceptor, retinal dehydrogenase
#2: Chemical ChemComp-YB / YTTERBIUM (III) ION


Mass: 173.040 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Yb
#3: Chemical ChemComp-6ZY / 2,3,5-trimethyl-6-[3-oxo-3-(piperidin-1-yl)propyl]-7H-furo[3,2-g][1]benzopyran-7-one


Mass: 367.438 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H25NO4
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 309 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.27 Å3/Da / Density % sol: 45.92 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop
Details: 100 mM BisTris, 200 mM NaCl, 5 mM YbCl3, 9-11% PEG3350
PH range: 6.2-6.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 2, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 54446 / % possible obs: 97.6 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 9.6
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.501 / % possible all: 97

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
PDB_EXTRACT3.2data extraction
HKL-3000data reduction
RefinementResolution: 1.7→48.78 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.94 / SU B: 6.934 / SU ML: 0.122 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.131 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING
RfactorNum. reflection% reflectionSelection details
Rfree0.238 2762 5.1 %RANDOM
Rwork0.218 ---
obs0.219 51675 97.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.47 Å2
Baniso -1Baniso -2Baniso -3
1-0.57 Å20 Å20 Å2
2--0.57 Å20 Å2
3----1.13 Å2
Refinement stepCycle: LAST / Resolution: 1.7→48.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3789 0 29 309 4127
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0193927
X-RAY DIFFRACTIONr_bond_other_d0.0010.023730
X-RAY DIFFRACTIONr_angle_refined_deg1.3951.9695332
X-RAY DIFFRACTIONr_angle_other_deg0.7838601
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9165499
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.48124.699166
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.96415650
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4841517
X-RAY DIFFRACTIONr_chiral_restr0.0780.2587
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214481
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02872
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_it0.4081.0011984
X-RAY DIFFRACTIONr_mcbond_other0.4061.0011983
X-RAY DIFFRACTIONr_mcangle_it0.6681.52481
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.74 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.348 205 -
Rwork0.345 3724 -
obs--96.96 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
16.9787-0.99540.66851.6598-0.72681.4682-0.3226-0.6145-1.07380.83750.13370.15670.07380.04130.18890.60940.160.22690.31660.37360.487452.6084-31.449928.5829
22.00430.6316-0.42962.4772-0.35740.2699-0.2115-0.4907-0.42610.53830.05170.082-0.04190.06260.15980.18950.11080.08710.14160.1110.15955.9336-16.888617.1305
32.63230.682-0.72863.2466-1.27991.8125-0.3678-0.6234-0.20680.53280.1590.7642-0.01350.02720.20880.21650.14160.26170.18340.11080.417427.8234-10.435221.2541
41.74261.5588-0.73354.1532-1.85622.6861-0.0190.02190.25880.42380.23890.0914-0.1209-0.1666-0.21990.07280.0321-0.03260.02320.00730.088267.90022.62165.4699
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 61
2X-RAY DIFFRACTION2A62 - 270
3X-RAY DIFFRACTION3A271 - 482
4X-RAY DIFFRACTION4A483 - 501

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