[English] 日本語
Yorodumi
- PDB-9r6n: Crystal structure of ALDH1A2 in complex with KyA33 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9r6n
TitleCrystal structure of ALDH1A2 in complex with KyA33
ComponentsRetinal dehydrogenase 2
KeywordsOXIDOREDUCTASE / Inhibitor
Function / homology
Function and homology information


determination of bilateral symmetry / regulation of vascular endothelial cell proliferation / 3-chloroallyl aldehyde dehydrogenase activity / 9-cis-retinoic acid biosynthetic process / retinoic acid biosynthetic process / retinal dehydrogenase / ureter maturation / embryonic camera-type eye development / midgut development / morphogenesis of embryonic epithelium ...determination of bilateral symmetry / regulation of vascular endothelial cell proliferation / 3-chloroallyl aldehyde dehydrogenase activity / 9-cis-retinoic acid biosynthetic process / retinoic acid biosynthetic process / retinal dehydrogenase / ureter maturation / embryonic camera-type eye development / midgut development / morphogenesis of embryonic epithelium / pituitary gland development / RA biosynthesis pathway / proximal/distal pattern formation / vitamin A metabolic process / neural crest cell development / hindbrain development / retinal metabolic process / embryonic digestive tract development / aldehyde dehydrogenase (NAD+) activity / retinal binding / pancreas development / retinal dehydrogenase (NAD+) activity / embryonic forelimb morphogenesis / response to vitamin A / retinoic acid metabolic process / retinol metabolic process / cardiac muscle tissue development / anterior/posterior pattern specification / neural tube development / blood vessel development / face development / response to retinoic acid / heart morphogenesis / retinoic acid receptor signaling pathway / cellular response to retinoic acid / response to cytokine / lung development / kidney development / liver development / neuron differentiation / response to estradiol / protein homotetramerization / cell population proliferation / positive regulation of apoptotic process / negative regulation of cell population proliferation / positive regulation of cell population proliferation / positive regulation of gene expression / perinuclear region of cytoplasm / cytoplasm / cytosol
Similarity search - Function
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
Similarity search - Domain/homology
: / Retinal dehydrogenase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.4 Å
AuthorsFang, C. / Esposito, M. / Huang, J. / Kang, Y.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Manuscript in preparation
Authors: Kang, Y.
History
DepositionMay 13, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 19, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Retinal dehydrogenase 2
B: Retinal dehydrogenase 2
C: Retinal dehydrogenase 2
D: Retinal dehydrogenase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)220,54541
Polymers217,2594
Non-polymers3,28637
Water57,5403194
1
A: Retinal dehydrogenase 2
C: Retinal dehydrogenase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,36522
Polymers108,6292
Non-polymers1,73620
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8520 Å2
ΔGint23 kcal/mol
Surface area34350 Å2
2
B: Retinal dehydrogenase 2
D: Retinal dehydrogenase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,17919
Polymers108,6292
Non-polymers1,55017
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8180 Å2
ΔGint19 kcal/mol
Surface area34630 Å2
Unit cell
Length a, b, c (Å)81.639, 140.045, 84.775
Angle α, β, γ (deg.)90.00, 93.93, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Retinal dehydrogenase 2 / RALDH 2 / RalDH2 / Aldehyde dehydrogenase family 1 member A2 / ALDH1A2 / Retinaldehyde-specific ...RALDH 2 / RalDH2 / Aldehyde dehydrogenase family 1 member A2 / ALDH1A2 / Retinaldehyde-specific dehydrogenase type 2 / RALDH(II)


Mass: 54314.730 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ALDH1A2, RALDH2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIPL / References: UniProt: O94788, retinal dehydrogenase
#2: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 33 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-A1IDQ / 3-ethyl-~{N}-(8-methyl-2-oxidanylidene-3,4-dihydro-1~{H}-quinolin-6-yl)pyridine-4-carboxamide


Mass: 309.362 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C18H19N3O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3194 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.23 Å3/Da / Density % sol: 44.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M L-Proline, 0.1 M HEPES-NaOH pH 7.50, 10% w/v PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.965459 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jul 21, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.965459 Å / Relative weight: 1
ReflectionResolution: 1.4→30 Å / Num. obs: 365896 / % possible obs: 98.5 % / Redundancy: 6.8 % / CC1/2: 0.996 / Rmerge(I) obs: 0.105 / Rpim(I) all: 0.043 / Rrim(I) all: 0.113 / Net I/σ(I): 9.3 / Num. measured all: 2497266
Reflection shellResolution: 1.4→1.48 Å / % possible obs: 97 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.635 / Num. measured all: 370489 / Num. unique obs: 52541 / CC1/2: 0.801 / Rpim(I) all: 0.258 / Rrim(I) all: 0.686 / Net I/σ(I) obs: 2.9

-
Processing

Software
NameVersionClassification
DIALS3.8.0data reduction
SCALA3.3.22data scaling
REFMAC5.8.0352phasing
REFMAC5.8.0352refinement
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.4→29.82 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.964 / SU B: 2.029 / SU ML: 0.041 / Cross valid method: THROUGHOUT / ESU R: 0.059 / ESU R Free: 0.059 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1767 18629 5.1 %RANDOM
Rwork0.15573 ---
obs0.15682 346817 98.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 12.619 Å2
Baniso -1Baniso -2Baniso -3
1-0.82 Å20 Å2-0.07 Å2
2--0.06 Å20 Å2
3----0.86 Å2
Refinement stepCycle: 1 / Resolution: 1.4→29.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15250 0 224 3194 18668
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.01216283
X-RAY DIFFRACTIONr_bond_other_d0.0010.01615032
X-RAY DIFFRACTIONr_angle_refined_deg1.0191.65422093
X-RAY DIFFRACTIONr_angle_other_deg0.3671.56135157
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.44952118
X-RAY DIFFRACTIONr_dihedral_angle_2_deg4.2135107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.517102772
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0540.22391
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0219168
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023252
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_it0.6040.9248044
X-RAY DIFFRACTIONr_mcbond_other0.6040.9248045
X-RAY DIFFRACTIONr_mcangle_it0.9661.38610087
X-RAY DIFFRACTIONr_mcangle_other0.9661.38610088
X-RAY DIFFRACTIONr_scbond_it1.1951.1078239
X-RAY DIFFRACTIONr_scbond_other1.1951.1078240
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.8281.58811929
X-RAY DIFFRACTIONr_long_range_B_refined5.72923.03620195
X-RAY DIFFRACTIONr_long_range_B_other4.98114.13818629
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.4→1.436 Å
RfactorNum. reflection% reflection
Rfree0.24 1317 -
Rwork0.224 24730 -
obs--94.97 %
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)
10.05570.03340.09060.1442-0.03970.26030.0238-0.0117-0.00190.0166-0.02020.00110.0096-0.0055-0.00360.0236-0.00580.00430.02130.00590.0266435.875-138.404130.427
20.0809-0.0120.02460.25760.06080.11890.02060.0199-0.0243-0.0376-0.02680.05690.0041-0.00720.00610.01760.0068-0.02040.0182-0.01730.0482408.981-150.91690.577
30.08620.0001-0.01870.1993-0.01840.11730.0033-0.02460.01270.02230.00280.0512-0.0231-0.0166-0.00620.0130.00790.01830.0269-0.00940.0548405.981-118.501121.878
40.0697-0.0484-0.09180.1157-0.0120.21050.03520.00940.0023-0.0302-0.0267-0.0057-0.02960.0001-0.00850.03490.0120.00840.02240.00740.0214439.055-129.73886.357
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A29 - 999
2X-RAY DIFFRACTION2B20 - 999
3X-RAY DIFFRACTION3C20 - 999
4X-RAY DIFFRACTION4D20 - 999

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more