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- PDB-5l2o: Crystal Structure of ALDH1A1 in complex with BUC22 -

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Basic information

Entry
Database: PDB / ID: 5l2o
TitleCrystal Structure of ALDH1A1 in complex with BUC22
ComponentsRetinal dehydrogenase 1
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / ALDH1A1 Inhibitor / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex
Function / homology
Function and homology information


fructosamine catabolic process / 3-deoxyglucosone dehydrogenase activity / benzaldehyde dehydrogenase (NAD+) / benzaldehyde dehydrogenase (NAD+) activity / maintenance of lens transparency / retinal dehydrogenase / gamma-aminobutyric acid biosynthetic process / aminobutyraldehyde dehydrogenase / aminobutyraldehyde dehydrogenase (NAD+) activity / Fructose catabolism ...fructosamine catabolic process / 3-deoxyglucosone dehydrogenase activity / benzaldehyde dehydrogenase (NAD+) / benzaldehyde dehydrogenase (NAD+) activity / maintenance of lens transparency / retinal dehydrogenase / gamma-aminobutyric acid biosynthetic process / aminobutyraldehyde dehydrogenase / aminobutyraldehyde dehydrogenase (NAD+) activity / Fructose catabolism / Ethanol oxidation / aldehyde metabolic process / RA biosynthesis pathway / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (non-phosphorylating) activity / aldehyde dehydrogenase (NAD+) / cellular detoxification of aldehyde / androgen binding / aldehyde dehydrogenase (NAD+) activity / retinal dehydrogenase 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
7-(diethylamino)-4-methyl-2H-1-benzopyran-2-one / YTTERBIUM (III) ION / Aldehyde dehydrogenase 1A1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.05 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 1.4Mar 6, 2024Group: 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_struct_conn_angle / struct_conn / struct_ncs_dom_lim
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_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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_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_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.ptnr3_symmetry / _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.ptnr1_symmetry / _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_symmetry / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Retinal dehydrogenase 1
B: Retinal dehydrogenase 1
C: Retinal dehydrogenase 1
D: Retinal dehydrogenase 1
E: Retinal dehydrogenase 1
F: Retinal dehydrogenase 1
G: Retinal dehydrogenase 1
H: Retinal dehydrogenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)442,91532
Polymers439,3978
Non-polymers3,51824
Water41,9032326
1
A: Retinal dehydrogenase 1
B: Retinal dehydrogenase 1
C: Retinal dehydrogenase 1
D: Retinal dehydrogenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)221,28515
Polymers219,6984
Non-polymers1,58611
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22010 Å2
ΔGint-146 kcal/mol
Surface area60380 Å2
MethodPISA
2
E: Retinal dehydrogenase 1
F: Retinal dehydrogenase 1
G: Retinal dehydrogenase 1
H: Retinal dehydrogenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)221,63117
Polymers219,6984
Non-polymers1,93213
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22610 Å2
ΔGint-166 kcal/mol
Surface area60510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.984, 98.292, 127.322
Angle α, β, γ (deg.)80.550, 86.230, 64.360
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16A
26G
17A
27H
18B
28C
19B
29D
110B
210E
111B
211F
112B
212G
113B
213H
114C
214D
115C
215E
116C
216F
117C
217G
118C
218H
119D
219E
120D
220F
121D
221G
122D
222H
123E
223F
124E
224G
125E
225H
126F
226G
127F
227H
128G
228H

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASPASPSERSERAA8 - 5018 - 501
21ASPASPSERSERBB8 - 5018 - 501
12LEULEUASNASNAA9 - 5009 - 500
22LEULEUASNASNCC9 - 5009 - 500
13LEULEUASNASNAA9 - 5009 - 500
23LEULEUASNASNDD9 - 5009 - 500
14LEULEUASNASNAA9 - 5009 - 500
24LEULEUASNASNEE9 - 5009 - 500
15LEULEUASNASNAA9 - 5009 - 500
25LEULEUASNASNFF9 - 5009 - 500
16ASPASPSERSERAA8 - 5018 - 501
26ASPASPSERSERGG8 - 5018 - 501
17LEULEUASNASNAA9 - 5009 - 500
27LEULEUASNASNHH9 - 5009 - 500
18LEULEUASNASNBB9 - 5009 - 500
28LEULEUASNASNCC9 - 5009 - 500
19LEULEUASNASNBB9 - 5009 - 500
29LEULEUASNASNDD9 - 5009 - 500
110LEULEUASNASNBB9 - 5009 - 500
210LEULEUASNASNEE9 - 5009 - 500
111LEULEUASNASNBB9 - 5009 - 500
211LEULEUASNASNFF9 - 5009 - 500
112ASPASPSERSERBB8 - 5018 - 501
212ASPASPSERSERGG8 - 5018 - 501
113LEULEUASNASNBB9 - 5009 - 500
213LEULEUASNASNHH9 - 5009 - 500
114LEULEUSERSERCC9 - 5019 - 501
214LEULEUSERSERDD9 - 5019 - 501
115LEULEUSERSERCC9 - 5019 - 501
215LEULEUSERSEREE9 - 5019 - 501
116LEULEUSERSERCC9 - 5019 - 501
216LEULEUSERSERFF9 - 5019 - 501
117LEULEUASNASNCC9 - 5009 - 500
217LEULEUASNASNGG9 - 5009 - 500
118LEULEUSERSERCC9 - 5019 - 501
218LEULEUSERSERHH9 - 5019 - 501
119LEULEUSERSERDD9 - 5019 - 501
219LEULEUSERSEREE9 - 5019 - 501
120LEULEUSERSERDD9 - 5019 - 501
220LEULEUSERSERFF9 - 5019 - 501
121LEULEUASNASNDD9 - 5009 - 500
221LEULEUASNASNGG9 - 5009 - 500
122LEULEUSERSERDD9 - 5019 - 501
222LEULEUSERSERHH9 - 5019 - 501
123LEULEUSERSEREE9 - 5019 - 501
223LEULEUSERSERFF9 - 5019 - 501
124LEULEUASNASNEE9 - 5009 - 500
224LEULEUASNASNGG9 - 5009 - 500
125LEULEUSERSEREE9 - 5019 - 501
225LEULEUSERSERHH9 - 5019 - 501
126LEULEUASNASNFF9 - 5009 - 500
226LEULEUASNASNGG9 - 5009 - 500
127LEULEUSERSERFF9 - 5019 - 501
227LEULEUSERSERHH9 - 5019 - 501
128LEULEUASNASNGG9 - 5009 - 500
228LEULEUASNASNHH9 - 5009 - 500

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28

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Components

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


Mass: 54924.617 Da / Num. of mol.: 8
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-6ZW / 7-(diethylamino)-4-methyl-2H-1-benzopyran-2-one


Mass: 231.290 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C14H17NO2
#3: Chemical
ChemComp-YB / YTTERBIUM (III) ION


Mass: 173.040 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Yb
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2326 / 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: 2.33 Å3/Da / Density % sol: 47.25 %
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: 2.05→50 Å / Num. obs: 222612 / % possible obs: 90.8 % / Redundancy: 2.1 % / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.061 / Rrim(I) all: 0.093 / Χ2: 0.934 / Net I/σ(I): 7.3 / Num. measured all: 461481
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.05-2.092.10.28112130.8450.2510.3770.78291.7
2.09-2.122.10.259111850.8620.2330.350.78191.4
2.12-2.162.10.224112020.8890.2020.3030.80590.9
2.16-2.212.10.204109960.910.1820.2740.81890.2
2.21-2.262.10.18108400.9290.1610.2420.82488.4
2.26-2.3120.159105590.9390.1420.2140.83286.2
2.31-2.3720.146103340.9460.130.1970.88284
2.37-2.432.10.135114490.9570.120.1810.86693.6
2.43-2.52.10.127115270.9610.1130.1710.89693.3
2.5-2.582.10.109114050.970.0960.1460.88592.9
2.58-2.682.10.098113190.9760.0870.1310.95992.4
2.68-2.782.10.091112290.9790.080.1221.00191.7
2.78-2.912.10.079109340.9830.0690.1051.01789.1
2.91-3.0620.068102320.9870.060.0911.12583.4
3.06-3.252.10.059117110.990.0520.0791.0395.3
3.25-3.512.10.049116220.9930.0430.0660.98494.7
3.51-3.862.10.041113970.9950.0360.0550.95793
3.86-4.4220.038106710.9950.0330.050.9687.2
4.42-5.562.10.036115850.9950.0320.0490.98694.3
5.56-502.10.043112020.9950.0380.0581.28891.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
PDB_EXTRACT3.2data extraction
HKL-3000data reduction
RefinementResolution: 2.05→50 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.93 / SU B: 4.477 / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.242 / ESU R Free: 0.174 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2045 11177 5 %RANDOM
Rwork0.1736 ---
obs0.1751 211433 90.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 81.09 Å2 / Biso mean: 19.814 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.19 Å21.37 Å2-1.11 Å2
2--0.6 Å20.01 Å2
3---0.61 Å2
Refinement stepCycle: final / Resolution: 2.05→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms30488 0 152 2326 32966
Biso mean--28.78 26.51 -
Num. residues----3947
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01931429
X-RAY DIFFRACTIONr_bond_other_d0.0070.0230154
X-RAY DIFFRACTIONr_angle_refined_deg1.3881.96642547
X-RAY DIFFRACTIONr_angle_other_deg1.238369608
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8653975
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.99524.7181329
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.627155389
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.54215136
X-RAY DIFFRACTIONr_chiral_restr0.0780.24685
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02135639
X-RAY DIFFRACTIONr_gen_planes_other0.0060.026965
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A313330.06
12B313330.06
21A311930.06
22C311930.06
31A309630.07
32D309630.07
41A311540.06
42E311540.06
51A309980.07
52F309980.07
61A311460.06
62G311460.06
71A314580.05
72H314580.05
81B312900.06
82C312900.06
91B311380.06
92D311380.06
101B312660.06
102E312660.06
111B309800.07
112F309800.07
121B312240.06
122G312240.06
131B311650.06
132H311650.06
141C311240.07
142D311240.07
151C313310.06
152E313310.06
161C312250.06
162F312250.06
171C312450.06
172G312450.06
181C312060.06
182H312060.06
191D313370.06
192E313370.06
201D310810.07
202F310810.07
211D310740.07
212G310740.07
221D311630.07
222H311630.07
231E313350.07
232F313350.07
241E312930.06
242G312930.06
251E313930.06
252H313930.06
261F310420.07
262G310420.07
271F311790.07
272H311790.07
281G312500.06
282H312500.06
LS refinement shellResolution: 2.051→2.104 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.247 794 -
Rwork0.223 15363 -
all-16157 -
obs--89.08 %

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