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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 / aminobutyraldehyde dehydrogenase activity / aminobutyraldehyde dehydrogenase / retinal dehydrogenase / maintenance of lens transparency / gamma-aminobutyric acid biosynthetic process / Fructose catabolism ...fructosamine catabolic process / 3-deoxyglucosone dehydrogenase activity / benzaldehyde dehydrogenase (NAD+) / benzaldehyde dehydrogenase (NAD+) activity / aminobutyraldehyde dehydrogenase activity / aminobutyraldehyde dehydrogenase / retinal dehydrogenase / maintenance of lens transparency / gamma-aminobutyric acid biosynthetic process / Fructose catabolism / Ethanol oxidation / RA biosynthesis pathway / cellular aldehyde metabolic process / aldehyde dehydrogenase (NAD+) / cellular detoxification of aldehyde / androgen binding / aldehyde dehydrogenase (NAD+) activity / retinal dehydrogenase activity / negative regulation of cold-induced thermogenesis / retinoid metabolic process / retinol metabolic process / GTPase activator activity / NAD binding / axon / synapse / extracellular exosome / cytosol / cytoplasm
Similarity search - Function
Aldehyde dehydrogenases cysteine active site. / Aldehyde dehydrogenase, cysteine active site / 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 dehydrogenases glutamic acid active site. / Aldehyde dehydrogenase, glutamic acid active site / Aldehyde dehydrogenase, N-terminal / Aldehyde dehydrogenase family ...Aldehyde dehydrogenases cysteine active site. / Aldehyde dehydrogenase, cysteine active site / 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 dehydrogenases glutamic acid active site. / Aldehyde dehydrogenase, glutamic acid active site / Aldehyde dehydrogenase, N-terminal / Aldehyde dehydrogenase family / Aldehyde dehydrogenase, C-terminal / Aldehyde dehydrogenase domain / 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

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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
γ
α
β
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:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A8 - 501
2010B8 - 501
1020A9 - 500
2020C9 - 500
1030A9 - 500
2030D9 - 500
1040A9 - 500
2040E9 - 500
1050A9 - 500
2050F9 - 500
1060A8 - 501
2060G8 - 501
1070A9 - 500
2070H9 - 500
1080B9 - 500
2080C9 - 500
1090B9 - 500
2090D9 - 500
10100B9 - 500
20100E9 - 500
10110B9 - 500
20110F9 - 500
10120B8 - 501
20120G8 - 501
10130B9 - 500
20130H9 - 500
10140C9 - 501
20140D9 - 501
10150C9 - 501
20150E9 - 501
10160C9 - 501
20160F9 - 501
10170C9 - 500
20170G9 - 500
10180C9 - 501
20180H9 - 501
10190D9 - 501
20190E9 - 501
10200D9 - 501
20200F9 - 501
10210D9 - 500
20210G9 - 500
10220D9 - 501
20220H9 - 501
10230E9 - 501
20230F9 - 501
10240E9 - 500
20240G9 - 500
10250E9 - 501
20250H9 - 501
10260F9 - 500
20260G9 - 500
10270F9 - 501
20270H9 - 501
10280G9 - 500
20280H9 - 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 / Ytterbium


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


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