[English] 日本語
Yorodumi
- PDB-1eko: PIG ALDOSE REDUCTASE COMPLEXED WITH IDD384 INHIBITOR -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1eko
TitlePIG ALDOSE REDUCTASE COMPLEXED WITH IDD384 INHIBITOR
ComponentsALDOSE REDUCTASE
KeywordsOXIDOREDUCTASE / ALDOSE REDUCTASE / INHIBITION / DIABETES
Function / homology
Function and homology information


glycerol dehydrogenase [NADP+] activity / D/L-glyceraldehyde reductase / aldose reductase / NADP-retinol dehydrogenase / allyl-alcohol dehydrogenase activity / allyl-alcohol dehydrogenase / prostaglandin H2 endoperoxidase reductase activity / NADP-retinol dehydrogenase activity / retinal dehydrogenase activity / retinoid metabolic process ...glycerol dehydrogenase [NADP+] activity / D/L-glyceraldehyde reductase / aldose reductase / NADP-retinol dehydrogenase / allyl-alcohol dehydrogenase activity / allyl-alcohol dehydrogenase / prostaglandin H2 endoperoxidase reductase activity / NADP-retinol dehydrogenase activity / retinal dehydrogenase activity / retinoid metabolic process / alditol:NADP+ 1-oxidoreductase activity / cytoplasm
Similarity search - Function
Aldo/keto reductase family putative active site signature. / Aldo/keto reductase family signature 1. / Aldo/keto reductase family signature 2. / Aldo/keto reductase, conserved site / NADP-dependent oxidoreductase domain / Aldo-keto reductase / NADP-dependent oxidoreductase domain / Aldo/keto reductase family / NADP-dependent oxidoreductase domain superfamily / TIM Barrel ...Aldo/keto reductase family putative active site signature. / Aldo/keto reductase family signature 1. / Aldo/keto reductase family signature 2. / Aldo/keto reductase, conserved site / NADP-dependent oxidoreductase domain / 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
Chem-I84 / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Aldo-keto reductase family 1 member B1
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsPodjarny, A.
Citation
#1: Journal: J.AM.SOC.MASS.SPECTROM. / Year: 1999
Title: Binding of Aldose Reductase Inhibitors: Correlation of Crystallographic and Mass Spectrometric Studies
Authors: Rogniaux, H. / Van Dorsselaer, A. / Barth, P. / Biellmann, J.F. / Barbanton, J. / van Zandt, M. / Chevrier, B. / Howard, E. / Mitschler, A. / Potier, N. / Urzhumtseva, L. / Moras, D. / Podjarny, A.
History
DepositionMar 9, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 10, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ALDOSE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9583
Polymers35,8241
Non-polymers1,1342
Water1,27971
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.810, 68.810, 154.770
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

-
Components

#1: Protein ALDOSE REDUCTASE /


Mass: 35824.035 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: EYE / Tissue: LENS / References: UniProt: P80276, aldose reductase
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical ChemComp-I84 / [2,6-DIMETHYL-4-(2-O-TOLYL-ACETYLAMINO)-BENZENESULFONYL]-GLYCINE / INHIBITOR IDD 384


Mass: 390.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H22N2O5S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 71 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.56 Å3/Da / Density % sol: 51.87 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 6 MG/ML AR, 2.5% PEG 6000, 25 MM MESPH 6.2 (DROP), 20% PEG 6000, 25 MM MESPH 6.2 (RESERVOIR) , VAPOR DIFFUSION, HANGING DROP, temperature 277.0K
Crystal grow
*PLUS
Details: Rogniaux, H., (1999) J. Am. Soc. Mass Spectrom., 10, 635.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115 mg/mlprotein1drop
3NADP+1drop
475 mMMES1drop
51 mMEDTA1drop
61 mMdithiothreitol1drop
72.5 %(w/v)PEG60001drop
825 %PEG60001reservoir
91
21
101

-
Data collection

DiffractionMean temperature: 273 K
Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.91
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 8, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91 Å / Relative weight: 1
ReflectionResolution: 2.2→15 Å / Num. all: 20372 / Num. obs: 19184 / % possible obs: 98.1 % / Observed criterion σ(F): 6 / Observed criterion σ(I): 3 / Redundancy: 5 % / Biso Wilson estimate: 37.1 Å2 / Rmerge(I) obs: 0.086 / Rsym value: 0.086 / Net I/σ(I): 22.5
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.245 / Mean I/σ(I) obs: 3.1 / Rsym value: 0.245 / % possible all: 97.5

-
Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.851refinement
XDSdata reduction
AUTOMARdata reduction
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: ALDOSE REDUCTASE NATIVE

Resolution: 2.2→8 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 18314069.48 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 1 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.273 1801 9.8 %RANDOM
Rwork0.216 ---
all0.221 20372 --
obs0.216 18338 95.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 70.8234 Å2 / ksol: 0.382389 e/Å3
Displacement parametersBiso mean: 42.4 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.31 Å
Luzzati d res low-8 Å
Luzzati sigma a0.42 Å0.4 Å
Refinement stepCycle: LAST / Resolution: 2.2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2523 0 75 71 2669
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_dihedral_angle_d27.8
X-RAY DIFFRACTIONx_improper_angle_d0.72
X-RAY DIFFRACTIONx_mcbond_it1.981.5
X-RAY DIFFRACTIONx_mcangle_it3.122
X-RAY DIFFRACTIONx_scbond_it3.332
X-RAY DIFFRACTIONx_scangle_it4.822.5
LS refinement shellResolution: 2.2→2.3 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.394 240 11 %
Rwork0.355 1950 -
obs--93.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP_PARAMTOPHCSDX_PLUS.PRO
X-RAY DIFFRACTION2NADP.PARAMNADP.TOPOL
X-RAY DIFFRACTION3I0384.PARAMI0384.TOPOL
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 8 Å / σ(F): 2 / % reflection Rfree: 9.8 % / Rfactor obs: 0.179
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 42.4 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.8
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.72
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scangle_it2.5
LS refinement shell
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 2.3 Å / Rfactor Rfree: 0.394 / % reflection Rfree: 11 % / Rfactor Rwork: 0.355

+
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