[English] 日本語
Yorodumi
- PDB-5m2f: Crystal structure of human AKR1B10 complexed with NADP+ and the s... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5m2f
TitleCrystal structure of human AKR1B10 complexed with NADP+ and the synthetic retinoid UVI2008
ComponentsAldo-keto reductase family 1 member B10
KeywordsOXIDOREDUCTASE / TIM barrel / Aldo-Keto Reductase / Synthetic Retinoid / Cytosolic
Function / homology
Function and homology information


indanol dehydrogenase activity / alcohol dehydrogenase (NADP+) activity / farnesol catabolic process / geranylgeranyl reductase activity / cellular detoxification of aldehyde / aldo-keto reductase (NADP) activity / NADP-retinol dehydrogenase / allyl-alcohol dehydrogenase / allyl-alcohol dehydrogenase activity / NADP-retinol dehydrogenase activity ...indanol dehydrogenase activity / alcohol dehydrogenase (NADP+) activity / farnesol catabolic process / geranylgeranyl reductase activity / cellular detoxification of aldehyde / aldo-keto reductase (NADP) activity / NADP-retinol dehydrogenase / allyl-alcohol dehydrogenase / allyl-alcohol dehydrogenase activity / NADP-retinol dehydrogenase activity / daunorubicin metabolic process / doxorubicin metabolic process / retinal dehydrogenase activity / retinoid metabolic process / alditol:NADP+ 1-oxidoreductase activity / Retinoid metabolism and transport / lysosome / mitochondrion / extracellular region / 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 / 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
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Chem-UV8 / Aldo-keto reductase family 1 member B10
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.503 Å
AuthorsRuiz, F.X. / Cousido-Siah, A. / Mitschler, A. / Porte, S. / Alvarez, S. / Dominguez, M. / Alvarez, R. / de Lera, A.R. / Pares, X. / Farres, J. / Podjarny, A.
CitationJournal: Chem. Biol. Interact. / Year: 2017
Title: Structural basis for the inhibition of AKR1B10 by the C3 brominated TTNPB derivative UVI2008.
Authors: Ruiz, F.X. / Crespo, I. / Alvarez, S. / Porte, S. / Gimenez-Dejoz, J. / Cousido-Siah, A. / Mitschler, A. / de Lera, A.R. / Pares, X. / Podjarny, A. / Farres, J.
History
DepositionOct 12, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 15, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
X: Aldo-keto reductase family 1 member B10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,6804
Polymers36,4471
Non-polymers1,2333
Water2,126118
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1440 Å2
ΔGint-2 kcal/mol
Surface area13790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.475, 79.475, 49.823
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

-
Components

#1: Protein Aldo-keto reductase family 1 member B10 / ARL-1 / Aldose reductase-like / Aldose reductase-related protein / hARP / Small intestine reductase ...ARL-1 / Aldose reductase-like / Aldose reductase-related protein / hARP / Small intestine reductase / SI reductase


Mass: 36447.121 Da / Num. of mol.: 1 / Mutation: K125R, V301L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AKR1B10, AKR1B11 / Production host: Escherichia coli (E. coli)
References: UniProt: O60218, Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor
#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-UV8 / 3-bromo-4-[(1E)-2-(5,5,8,8-tetramethyl-5,6,7,8-tetrahydronaphthalen-2-yl)prop-1-en-1-yl]benzoic acid


Mass: 427.374 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H27BrO2
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 118 / 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: 2.49 Å3/Da / Density % sol: 50.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9 / Details: 30% PEG 6000, 100 mM sodium cacodylate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.729 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 16, 2013
RadiationMonochromator: BARTELS MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.729 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 55875 / % possible obs: 99.66 % / Redundancy: 2.6 % / Rsym value: 0.055 / Net I/σ(I): 16.9
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 2.3 / % possible all: 98.22

-
Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
Cootmodel building
PHASERphasing
PHENIX1.8_1069refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ZUA

1zua


Resolution: 1.503→40.359 Å / Cross valid method: FREE R-VALUE / σ(F): 2.69 / Phase error: 24.42
RfactorNum. reflection% reflectionSelection details
Rfree0.2407 2890 5.17 %Random 5%
Rwork0.21 ---
obs0.212 55875 99.66 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.503→40.359 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2573 0 79 118 2770
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072768
X-RAY DIFFRACTIONf_angle_d1.1753768
X-RAY DIFFRACTIONf_dihedral_angle_d14.4981086
X-RAY DIFFRACTIONf_chiral_restr0.074402
X-RAY DIFFRACTIONf_plane_restr0.005469
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5026-1.52850.22811560.26482562X-RAY DIFFRACTION93
1.5285-1.55630.23281280.24572687X-RAY DIFFRACTION95
1.5563-1.58620.2361570.252600X-RAY DIFFRACTION94
1.5862-1.61860.23921420.24732660X-RAY DIFFRACTION94
1.6186-1.65370.2411500.25462641X-RAY DIFFRACTION95
1.6537-1.69220.22771700.25072606X-RAY DIFFRACTION93
1.6922-1.73450.25291000.2512704X-RAY DIFFRACTION96
1.7345-1.78130.27761400.25952637X-RAY DIFFRACTION95
1.7813-1.83370.24181480.24692674X-RAY DIFFRACTION95
1.8337-1.89290.27161320.24982650X-RAY DIFFRACTION95
1.8929-1.96050.22411800.24022601X-RAY DIFFRACTION93
1.9605-2.03890.26471430.2312704X-RAY DIFFRACTION95
2.0389-2.13160.2481700.2342596X-RAY DIFFRACTION94
2.1316-2.24380.26371460.22932653X-RAY DIFFRACTION95
2.2438-2.38420.27991680.22662643X-RAY DIFFRACTION94
2.3842-2.56790.26411480.22922663X-RAY DIFFRACTION95
2.5679-2.82570.27161480.22752651X-RAY DIFFRACTION95
2.8257-3.2330.27381220.20082671X-RAY DIFFRACTION96
3.233-4.06750.2031320.16492680X-RAY DIFFRACTION95
4.0675-19.87050.18861100.15822681X-RAY DIFFRACTION96

+
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