[English] 日本語
Yorodumi
- PDB-4q7b: Human Aldose Reductase complexed with a ligand with an IDD struct... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4q7b
TitleHuman Aldose Reductase complexed with a ligand with an IDD structure ([2-(benzylcarbamoyl)-5-fluorophenoxy]acetic acid) at 1.19 A
ComponentsAldose reductase
Keywordsoxidoreductase/oxidoreductase inhibitor / TIM BARREL / OXIDOREDUCTASE / oxidoreductase-oxidoreductase inhibitor 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 / Pregnenolone biosynthesis / NADP-retinol dehydrogenase ...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 / Pregnenolone biosynthesis / NADP-retinol dehydrogenase / allyl-alcohol dehydrogenase / allyl-alcohol dehydrogenase activity / L-ascorbic acid biosynthetic process / metanephric collecting duct development / prostaglandin H2 endoperoxidase reductase activity / regulation of urine volume / all-trans-retinol dehydrogenase (NADP+) activity / daunorubicin metabolic process / doxorubicin metabolic process / retinal dehydrogenase activity / epithelial cell maturation / aldose reductase (NADPH) activity / retinoid metabolic process / cellular hyperosmotic salinity response / renal water homeostasis / carbohydrate metabolic process / electron transfer activity / negative regulation of apoptotic process / 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
[2-(benzylcarbamoyl)-5-fluorophenoxy]acetic acid / 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: 1.19 Å
AuthorsRechlin, C. / Heine, A. / Klebe, G.
CitationJournal: To be Published
Title: Aldose Reductase: How expensive is the opening of the specificity pocket? IDD ligands under investigation
Authors: Rechlin, C. / Heine, A. / Scheer, F. / Toth, P. / Diederich, W. / Klebe, G.
History
DepositionApr 24, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Aldose reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8143
Polymers35,7671
Non-polymers1,0472
Water6,666370
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.317, 66.739, 47.254
Angle α, β, γ (deg.)90.00, 92.07, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

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


Mass: 35767.145 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AKR1B1, ALDR1 / Plasmid: PET15B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 gold / 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-2YZ / [2-(benzylcarbamoyl)-5-fluorophenoxy]acetic acid


Mass: 303.285 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H14FNO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 370 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE CONFLICT IS REPORTED IN THE UNPROT P15121

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.17 Å3/Da / Density % sol: 43.39 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Crystallization solution: 50 mM di-Ammoniumhydrogen citrate pH 5.0 PEG6000= 5 % (m/V) DTT= 5,15 g/L NADP+= 0,66 g/L and Human Aldose Reductase= 15 mg/ml. Afterwards the crystals were soaked ...Details: Crystallization solution: 50 mM di-Ammoniumhydrogen citrate pH 5.0 PEG6000= 5 % (m/V) DTT= 5,15 g/L NADP+= 0,66 g/L and Human Aldose Reductase= 15 mg/ml. Afterwards the crystals were soaked into Tris 100 mM 25% (m/V) PEG6000 saturated with the inhibitor, VAPOR DIFFUSION, HANGING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 13, 2013 / Details: Silicon, active surface 50 nm Rh-coated
RadiationMonochromator: Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.19→50 Å / Num. all: 97712 / Num. obs: 97712 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 7.728 Å2 / Rsym value: 0.055 / Net I/σ(I): 20
Reflection shellResolution: 1.19→1.21 Å / Redundancy: 3 % / Mean I/σ(I) obs: 2.48 / Rsym value: 0.446 / % possible all: 98.9

-
Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2dux

2dux


Resolution: 1.19→18.733 Å / SU ML: 0.1 / σ(F): 1.35 / Phase error: 14.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1603 4879 4.99 %
Rwork0.1376 --
obs0.1388 97683 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.19→18.733 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2483 0 70 370 2923
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062702
X-RAY DIFFRACTIONf_angle_d1.2423702
X-RAY DIFFRACTIONf_dihedral_angle_d15.0421009
X-RAY DIFFRACTIONf_chiral_restr0.077412
X-RAY DIFFRACTIONf_plane_restr0.007473
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1899-1.20340.21791380.20573032X-RAY DIFFRACTION97
1.2034-1.21760.26431600.19653071X-RAY DIFFRACTION100
1.2176-1.23240.19431620.17873092X-RAY DIFFRACTION100
1.2324-1.2480.18391380.17063063X-RAY DIFFRACTION100
1.248-1.26440.20031550.16823135X-RAY DIFFRACTION100
1.2644-1.28170.1871520.15753079X-RAY DIFFRACTION100
1.2817-1.30.20271610.15483093X-RAY DIFFRACTION100
1.3-1.31940.19491490.14963106X-RAY DIFFRACTION100
1.3194-1.34010.17271500.14713101X-RAY DIFFRACTION100
1.3401-1.3620.18381840.14343100X-RAY DIFFRACTION100
1.362-1.38550.17831510.1363064X-RAY DIFFRACTION100
1.3855-1.41070.1581560.13083090X-RAY DIFFRACTION100
1.4107-1.43780.15831660.12723081X-RAY DIFFRACTION100
1.4378-1.46710.15261660.12683079X-RAY DIFFRACTION100
1.4671-1.4990.16781950.12293062X-RAY DIFFRACTION100
1.499-1.53390.14741700.11423075X-RAY DIFFRACTION100
1.5339-1.57220.13331930.11233063X-RAY DIFFRACTION100
1.5722-1.61470.14191630.10873082X-RAY DIFFRACTION100
1.6147-1.66220.14241730.11353099X-RAY DIFFRACTION100
1.6622-1.71580.14291540.12193086X-RAY DIFFRACTION100
1.7158-1.77710.15611720.12323097X-RAY DIFFRACTION100
1.7771-1.84820.15371710.12953081X-RAY DIFFRACTION100
1.8482-1.93220.13251840.13233091X-RAY DIFFRACTION100
1.9322-2.0340.16091800.13133079X-RAY DIFFRACTION100
2.034-2.16120.1481370.12883145X-RAY DIFFRACTION100
2.1612-2.32780.16591540.13873102X-RAY DIFFRACTION100
2.3278-2.56160.14241740.14293111X-RAY DIFFRACTION100
2.5616-2.9310.15581650.14953124X-RAY DIFFRACTION100
2.931-3.68810.15951450.14063149X-RAY DIFFRACTION100
3.6881-18.7350.15931610.13413172X-RAY DIFFRACTION99

+
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