[English] 日本語
Yorodumi
- PDB-2alr: ALDEHYDE REDUCTASE -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2alr
TitleALDEHYDE REDUCTASE
ComponentsALDEHYDE REDUCTASE
KeywordsOXIDOREDUCTASE / TIM-BARREL
Function / homology
Function and homology information


glucuronate reductase / glucuronolactone reductase / glucuronolactone reductase activity / Formation of xylulose-5-phosphate / D-glucuronate catabolic process to D-xylulose 5-phosphate / Oxidoreductases; Acting on NADH or NADPH / S-nitrosoglutathione reductase (NADPH) activity / S-nitrosoglutathione reductase (NADH) activity / alcohol dehydrogenase (NADP+) / aldehyde catabolic process ...glucuronate reductase / glucuronolactone reductase / glucuronolactone reductase activity / Formation of xylulose-5-phosphate / D-glucuronate catabolic process to D-xylulose 5-phosphate / Oxidoreductases; Acting on NADH or NADPH / S-nitrosoglutathione reductase (NADPH) activity / S-nitrosoglutathione reductase (NADH) activity / alcohol dehydrogenase (NADP+) / aldehyde catabolic process / methylglyoxal reductase (NADPH) (acetol producing) activity / glutathione derivative biosynthetic process / cellular detoxification of aldehyde / L-glucuronate reductase activity / D/L-glyceraldehyde reductase / glycerol dehydrogenase (NADP+) activity / Glutathione conjugation / : / allyl-alcohol dehydrogenase / allyl-alcohol dehydrogenase activity / daunorubicin metabolic process / doxorubicin metabolic process / aldose reductase (NADPH) activity / lipid metabolic process / apical plasma membrane / synapse / negative regulation of apoptotic process / extracellular space / extracellular exosome / cytosol
Similarity search - Function
Aldo-keto reductase family 1 member A1 / Aldo/keto reductase family putative active site signature. / Aldo/keto reductase family signature 1. / NADP-dependent oxidoreductase domain / Aldo/keto reductase family signature 2. / Aldo/keto reductase, conserved site / Aldo-keto reductase / NADP-dependent oxidoreductase domain / Aldo/keto reductase family / NADP-dependent oxidoreductase domain superfamily ...Aldo-keto reductase family 1 member A1 / Aldo/keto reductase family putative active site signature. / Aldo/keto reductase family signature 1. / NADP-dependent oxidoreductase domain / Aldo/keto reductase family signature 2. / Aldo/keto reductase, conserved site / Aldo-keto reductase / NADP-dependent oxidoreductase domain / Aldo/keto reductase family / NADP-dependent oxidoreductase domain superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Aldo-keto reductase family 1 member A1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.48 Å
AuthorsEl-Kabbani, O.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 1994
Title: Structures of human and porcine aldehyde reductase: an enzyme implicated in diabetic complications.
Authors: El-Kabbani, O. / Green, N.C. / Lin, G. / Carson, M. / Narayana, S.V. / Moore, K.M. / Flynn, T.G. / DeLucas, L.J.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1993
Title: Crystallization and Preliminary Structure Determination of Porcine Aldehyde Reductase from Two Crystal Forms
Authors: El-Kabbani, O. / Lin, G. / Narayana, S.V.L. / Moore, K.M. / Green, N.C. / Flynn, T.G. / Delucas, L.J.
History
DepositionSep 6, 1994Processing site: BNL
SupersessionJun 20, 1996ID: 1ALR
Revision 1.0Jun 20, 1996Provider: 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 / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ALDEHYDE REDUCTASE


Theoretical massNumber of molelcules
Total (without water)36,4871
Polymers36,4871
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.600, 60.000, 66.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein ALDEHYDE REDUCTASE / ALR1


Mass: 36486.770 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Organ: KIDNEY / Tissue: MEDULLA, CORTEX / References: UniProt: P14550, alcohol dehydrogenase (NADP+)

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.25 Å3/Da / Density % sol: 43 %
Crystal growpH: 6.2 / Details: pH 6.2
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 293 K / pH: 6.4 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 %ammonium salfate1drop
210 mMPIPES1drop
32 mM2-mercaptoethanol1drop
420 mMbeta-octylglucoside1drop
535 %ammonium sulfate1reservoir
650 mMPIPES1reservoir
72 mM2-mercaptoethanol1reservoir
820 mMbeta-octylglucoside1reservoir

-
Data collection

DiffractionMean temperature: 293 K
Diffraction sourceWavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Apr 14, 1992 / Details: COLLIMATOR
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 10591 / % possible obs: 92 % / Observed criterion σ(I): 0 / Redundancy: 0.98 % / Rmerge(I) obs: 0.083

-
Processing

Software
NameClassification
X-PLORmodel building
TNTrefinement
X-PLORrefinement
XENGENdata reduction
X-PLORphasing
RefinementResolution: 2.48→6 Å / σ(F): 4 /
RfactorNum. reflection
Rwork0.19 -
obs-9538
Refinement stepCycle: LAST / Resolution: 2.48→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2472 0 0 0 2472
Refine LS restraints
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_bond_d0.0060.02
X-RAY DIFFRACTIONt_angle_deg2.13
X-RAY DIFFRACTIONt_dihedral_angle_d17.815
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.0040.02
X-RAY DIFFRACTIONt_gen_planes0.0080.02
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.19
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
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