[English] 日本語
Yorodumi
- PDB-8fh9: Crystal Structure Of Aldose Reductase (AKR1B1) Complexed With NAD... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8fh9
TitleCrystal Structure Of Aldose Reductase (AKR1B1) Complexed With NADP+ And AT-007
ComponentsAldo-keto reductase family 1 member B1
KeywordsOXIDOREDUCTASE / Complex
Function / homology
Function and homology information


glyceraldehyde oxidoreductase activity / Fructose biosynthesis / fructose biosynthetic process / L-glucuronate reductase activity / aldose reductase / D/L-glyceraldehyde reductase / glycerol dehydrogenase (NADP+) activity / C21-steroid hormone biosynthetic process / NADP-retinol dehydrogenase / Pregnenolone biosynthesis ...glyceraldehyde oxidoreductase activity / Fructose biosynthesis / fructose biosynthetic process / L-glucuronate reductase activity / aldose reductase / D/L-glyceraldehyde reductase / glycerol dehydrogenase (NADP+) activity / C21-steroid hormone biosynthetic process / NADP-retinol dehydrogenase / Pregnenolone biosynthesis / allyl-alcohol dehydrogenase / allyl-alcohol dehydrogenase activity / L-ascorbic acid biosynthetic process / prostaglandin H2 endoperoxidase reductase activity / metanephric collecting duct development / regulation of urine volume / all-trans-retinol dehydrogenase (NADP+) activity / daunorubicin metabolic process / doxorubicin metabolic process / retinal dehydrogenase activity / aldose reductase (NADPH) activity / epithelial cell maturation / retinoid metabolic process / cellular hyperosmotic salinity response / renal water homeostasis / carbohydrate metabolic process / electron transfer activity / negative regulation of apoptotic process / mitochondrion / extracellular space / extracellular exosome / nucleoplasm / cytosol
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 / Aldo-keto reductase / NADP-dependent oxidoreductase domain / Aldo/keto reductase family / NADP-dependent oxidoreductase domain superfamily
Similarity search - Domain/homology
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Chem-XYK / Aldo-keto reductase family 1 member B1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsArenas, R. / Wilson, D.K.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: To Be Published
Title: Crystal Structure Of Aldose Reductase (AKR1B1) Complexed With NADP+ And AT-007
Authors: Arenas, R. / Wilson, D.K.
History
DepositionDec 13, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 20, 2023Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Aldo-keto reductase family 1 member B1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3778
Polymers35,8981
Non-polymers1,4797
Water2,666148
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.179, 46.888, 47.296
Angle α, β, γ (deg.)75.478, 67.366, 76.634
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein Aldo-keto reductase family 1 member B1 / Aldehyde reductase / Aldose reductase / AR


Mass: 35898.340 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AKR1B1, ALDR1, ALR2 / Production host: Escherichia coli BL21 (bacteria)
References: UniProt: P15121, NADP-retinol dehydrogenase, D/L-glyceraldehyde reductase, allyl-alcohol dehydrogenase, aldose reductase
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-XYK / (4-oxo-3-{[5-(trifluoromethyl)-1,3-benzothiazol-2-yl]methyl}-3,4-dihydrothieno[3,4-d]pyridazin-1-yl)acetic acid


Mass: 425.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H10F3N3O3S2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 148 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.19 Å3/Da / Density % sol: 43.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 25% PEG 3,350, 100 mM Bis-Tris

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 13, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.7→36.688 Å / Num. obs: 30424 / % possible obs: 90.7 % / Redundancy: 3.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.035 / Rpim(I) all: 0.035 / Rrim(I) all: 0.05 / Net I/σ(I): 14.4
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.187 / Num. unique obs: 1727 / CC1/2: 0.967 / Rpim(I) all: 0.187 / Rrim(I) all: 0.265

-
Processing

Software
NameVersionClassification
REFMAC5.8.0403refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→36.688 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.951 / WRfactor Rfree: 0.184 / WRfactor Rwork: 0.151 / SU B: 1.729 / SU ML: 0.058 / Average fsc free: 0.979 / Average fsc work: 0.9868 / Cross valid method: FREE R-VALUE / ESU R: 0.106 / ESU R Free: 0.1
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.1818 1516 4.983 %0.05
Rwork0.1501 28905 --
all0.152 ---
obs-30421 90.666 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 16.5 Å2
Baniso -1Baniso -2Baniso -3
1-0.172 Å2-0.032 Å20.58 Å2
2---0.761 Å2-0.495 Å2
3---0.717 Å2
Refinement stepCycle: LAST / Resolution: 1.7→36.688 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2517 0 96 148 2761
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0122681
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162535
X-RAY DIFFRACTIONr_angle_refined_deg1.9771.6583647
X-RAY DIFFRACTIONr_angle_other_deg0.6821.5725864
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0465314
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.875.71414
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg0.97652
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.22210457
X-RAY DIFFRACTIONr_dihedral_angle_6_deg17.91410114
X-RAY DIFFRACTIONr_chiral_restr0.1150.2404
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.023003
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02574
X-RAY DIFFRACTIONr_nbd_refined0.220.2548
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1940.22490
X-RAY DIFFRACTIONr_nbtor_refined0.1860.21329
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.21362
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.2124
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2050.215
X-RAY DIFFRACTIONr_nbd_other0.1850.240
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1750.29
X-RAY DIFFRACTIONr_mcbond_it1.941.4871259
X-RAY DIFFRACTIONr_mcbond_other1.9391.4881259
X-RAY DIFFRACTIONr_mcangle_it2.6492.6711572
X-RAY DIFFRACTIONr_mcangle_other2.6492.6711573
X-RAY DIFFRACTIONr_scbond_it3.3451.8251422
X-RAY DIFFRACTIONr_scbond_other3.3441.8261423
X-RAY DIFFRACTIONr_scangle_it5.1543.1762075
X-RAY DIFFRACTIONr_scangle_other5.1533.1762076
X-RAY DIFFRACTIONr_lrange_it6.0417.073080
X-RAY DIFFRACTIONr_lrange_other6.01916.6623063
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.7-1.7440.211950.16121740.16325200.9740.98290.03970.143
1.744-1.7920.1761150.14720080.14923540.9770.98590.18690.129
1.792-1.8440.2041060.13920290.14223560.9760.98790.61970.123
1.844-1.90.218940.14419600.14723130.9720.98688.80240.125
1.9-1.9620.1811000.14717600.14922050.9780.98584.35370.13
1.962-2.0310.188860.13518660.13821180.9780.98992.16240.124
2.031-2.1070.178900.14218180.14420720.9790.98892.08490.133
2.107-2.1930.183900.13717410.13919900.9790.98992.010.129
2.193-2.290.165960.13315860.13518790.9820.98989.51570.126
2.29-2.4020.153660.13215260.13318420.9820.98986.42780.128
2.402-2.5310.172810.13215420.13417290.9820.9993.86930.128
2.531-2.6840.194750.13414490.13716520.9760.98992.25180.131
2.684-2.8680.162790.13513530.13615510.9820.98992.32750.136
2.868-3.0960.155660.14611800.14714240.9850.98887.50.152
3.096-3.3890.177650.15112010.15313330.9820.98694.97370.162
3.389-3.7850.186610.16710320.16911690.9830.98493.49870.182
3.785-4.3630.161520.1569240.15610620.9860.98691.90210.175
4.363-5.3250.199410.1727930.1748950.9830.98793.18440.203
5.325-7.4520.248390.2256010.2276840.9770.97993.56730.253
7.452-36.6880.188190.1813620.1824030.9750.9794.54090.211

+
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