[English] 日本語
Yorodumi
- PDB-5ou0: Crystal structure of human AKR1B1 complexed with NADP+ and compound 37 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ou0
TitleCrystal structure of human AKR1B1 complexed with NADP+ and compound 37
ComponentsAldose reductase
KeywordsOXIDOREDUCTASE / alpha-beta TIM barrel / cytosol / aldo-keto reductase / pyrimido[4 / 5-c]quinolone-2-acetic acid scaffold
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 / prostaglandin H2 endoperoxidase reductase activity / regulation of urine volume / metanephric collecting duct development / all-trans-retinol dehydrogenase (NADP+) activity / daunorubicin metabolic process / doxorubicin metabolic process / retinal dehydrogenase (NAD+) activity / aldose reductase (NADPH) activity / epithelial cell maturation / cellular hyperosmotic salinity response / renal water homeostasis / retinoid metabolic process / 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. / 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 ...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
Chem-AV5 / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Aldo-keto reductase family 1 member B1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.94 Å
AuthorsCousido-Siah, A. / Ruiz, F.X. / Mitschler, A. / Metwally, K. / Podjarny, A.
CitationJournal: Eur J Med Chem / Year: 2018
Title: Design, synthesis, structure-activity relationships and X-ray structural studies of novel 1-oxopyrimido[4,5-c]quinoline-2-acetic acid derivatives as selective and potent inhibitors of human aldose reductase.
Authors: Crespo, I. / Gimenez-Dejoz, J. / Porte, S. / Cousido-Siah, A. / Mitschler, A. / Podjarny, A. / Pratsinis, H. / Kletsas, D. / Pares, X. / Ruiz, F.X. / Metwally, K. / Farres, J.
History
DepositionAug 23, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 9, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Aldose reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0223
Polymers35,8981
Non-polymers1,1232
Water7,548419
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1190 Å2
ΔGint-5 kcal/mol
Surface area13240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.758, 46.771, 47.157
Angle α, β, γ (deg.)76.45, 67.76, 78.18
Int Tables number1
Space group name H-MP1

-
Components

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


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 / Production host: Escherichia coli (E. coli) / References: UniProt: P15121, 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
#3: Chemical ChemComp-AV5 / 2-[5-(4-chlorophenyl)-3-methyl-1-oxidanylidene-pyrimido[4,5-c]quinolin-2-yl]ethanoic acid


Mass: 379.796 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H14ClN3O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 419 / 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: 2.18 Å3/Da / Density % sol: 43.57 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 20% PEG 6000, 50 mM MES, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 297K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.8 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jul 3, 2014
RadiationMonochromator: Bartels Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 0.94→31.5 Å / Num. obs: 181549 / % possible obs: 91.9 % / Redundancy: 3.3 % / Rrim(I) all: 0.025 / Net I/σ(I): 38.95
Reflection shellResolution: 0.94→0.97 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 4.2 / Num. unique obs: 14598 / Rrim(I) all: 0.27 / % possible all: 74.7

-
Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4IGS

4igs


Resolution: 0.94→31.5 Å / SU ML: 0.07 / Cross valid method: FREE R-VALUE / σ(F): 1.76 / Phase error: 12.14
RfactorNum. reflection% reflection
Rfree0.143 -5 %
Rwork0.1293 --
obs0.13 181549 91.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 0.94→31.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2525 0 75 419 3019
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0262876
X-RAY DIFFRACTIONf_angle_d1.9723961
X-RAY DIFFRACTIONf_dihedral_angle_d16.6191099
X-RAY DIFFRACTIONf_chiral_restr0.118430
X-RAY DIFFRACTIONf_plane_restr0.014502
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.9388-0.94940.23294040.20647740X-RAY DIFFRACTION62
0.9494-0.96060.21184680.19439462X-RAY DIFFRACTION75
0.9606-0.97230.19345440.176310352X-RAY DIFFRACTION82
0.9723-0.98460.17895940.163410874X-RAY DIFFRACTION87
0.9846-0.99760.15285220.148811438X-RAY DIFFRACTION90
0.9976-1.01120.15915220.140811340X-RAY DIFFRACTION91
1.0112-1.02570.15065800.133911570X-RAY DIFFRACTION91
1.0257-1.0410.14536040.121211604X-RAY DIFFRACTION92
1.041-1.05730.13116780.11611486X-RAY DIFFRACTION92
1.0573-1.07460.12126700.114811562X-RAY DIFFRACTION93
1.0746-1.09310.13616260.112511598X-RAY DIFFRACTION93
1.0931-1.1130.12575840.103811722X-RAY DIFFRACTION93
1.113-1.13440.11656100.105911742X-RAY DIFFRACTION93
1.1344-1.15760.11216020.101911702X-RAY DIFFRACTION94
1.1576-1.18270.10956140.102311790X-RAY DIFFRACTION94
1.1827-1.21030.12395760.101411968X-RAY DIFFRACTION94
1.2103-1.24050.11566380.101411876X-RAY DIFFRACTION95
1.2405-1.27410.12085760.103911904X-RAY DIFFRACTION95
1.2741-1.31160.12036440.107411926X-RAY DIFFRACTION95
1.3116-1.35390.13416200.104211926X-RAY DIFFRACTION95
1.3539-1.40230.11986960.108511914X-RAY DIFFRACTION96
1.4023-1.45840.12086620.104912114X-RAY DIFFRACTION96
1.4584-1.52480.12356420.107312160X-RAY DIFFRACTION96
1.5248-1.60520.13036440.111612046X-RAY DIFFRACTION97
1.6052-1.70580.14076520.11812132X-RAY DIFFRACTION97
1.7058-1.83740.15076380.131112228X-RAY DIFFRACTION97
1.8374-2.02230.14496860.132912186X-RAY DIFFRACTION97
2.0223-2.31490.14826760.141312174X-RAY DIFFRACTION97
2.3149-2.91620.1676740.15711798X-RAY DIFFRACTION94
2.9162-31.55160.15975000.149410588X-RAY DIFFRACTION84

+
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