[English] 日本語
Yorodumi
- PDB-1u7t: Crystal Structure of ABAD/HSD10 with a Bound Inhibitor -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1u7t
TitleCrystal Structure of ABAD/HSD10 with a Bound Inhibitor
Components3-hydroxyacyl-CoA dehydrogenase type II
KeywordsOXIDOREDUCTASE / PROTEIN-INHIBITOR COMPLEX / ROSSMANN FOLD
Function / homology
Function and homology information


brexanolone metabolic process / isoursodeoxycholate 7-beta-dehydrogenase (NAD+) activity / ursodeoxycholate 7-beta-dehydrogenase (NAD+) activity / 3-hydroxy-2-methylbutyryl-CoA dehydrogenase / 3-hydroxy-2-methylbutyryl-CoA dehydrogenase activity / rRNA processing in the mitochondrion / mitochondrial tRNA methylation / tRNA processing in the mitochondrion / mitochondrial ribonuclease P complex / mitochondrial tRNA 5'-end processing ...brexanolone metabolic process / isoursodeoxycholate 7-beta-dehydrogenase (NAD+) activity / ursodeoxycholate 7-beta-dehydrogenase (NAD+) activity / 3-hydroxy-2-methylbutyryl-CoA dehydrogenase / 3-hydroxy-2-methylbutyryl-CoA dehydrogenase activity / rRNA processing in the mitochondrion / mitochondrial tRNA methylation / tRNA processing in the mitochondrion / mitochondrial ribonuclease P complex / mitochondrial tRNA 5'-end processing / chenodeoxycholate 7-alpha-dehydrogenase (NAD+) activity / mitochondrial tRNA 3'-end processing / tRNA modification in the mitochondrion / 7alpha-hydroxysteroid dehydrogenase / 17-beta-hydroxysteroid dehydrogenase (NAD+) activity / cholate 7-alpha-dehydrogenase activity / C21-steroid hormone metabolic process / testosterone dehydrogenase [NAD(P)] activity / tRNA methyltransferase complex / 3-hydroxyacyl-CoA dehydrogenase / isoleucine catabolic process / 3alpha(17beta)-hydroxysteroid dehydrogenase (NAD+) / 3-hydroxyacyl-CoA dehydrogenase activity / bile acid biosynthetic process / 3alpha(or 20beta)-hydroxysteroid dehydrogenase / androstan-3-alpha,17-beta-diol dehydrogenase activity / testosterone dehydrogenase (NAD+) activity / Branched-chain amino acid catabolism / 17beta-estradiol 17-dehydrogenase / estradiol 17-beta-dehydrogenase [NAD(P)] activity / estrogen metabolic process / fatty acid beta-oxidation / mitochondrial nucleoid / androgen metabolic process / mitochondrion organization / fatty acid metabolic process / lipid metabolic process / protein homotetramerization / tRNA binding / mitochondrial matrix / mitochondrion / RNA binding / plasma membrane / cytoplasm
Similarity search - Function
short chain dehydrogenase / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Chem-TDT / 3-hydroxyacyl-CoA dehydrogenase type-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsKissinger, C.R. / Rejto, P.A. / Pelletier, L.A. / Showalter, R.E. / Villafranca, J.E.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: Crystal structure of human ABAD/HSD10 with a bound inhibitor: implications for design of Alzheimer's disease therapeutics
Authors: Kissinger, C.R. / Rejto, P.A. / Pelletier, L.A. / Thomson, J.A. / Showalter, R.E. / Abreo, M.A. / Agree, C.S. / Margosiak, S. / Meng, J.J. / Aust, R.M. / Vanderpool, D. / Li, B. / Tempczyk- ...Authors: Kissinger, C.R. / Rejto, P.A. / Pelletier, L.A. / Thomson, J.A. / Showalter, R.E. / Abreo, M.A. / Agree, C.S. / Margosiak, S. / Meng, J.J. / Aust, R.M. / Vanderpool, D. / Li, B. / Tempczyk-Russell, A. / Villafranca, J.E.
History
DepositionAug 4, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.6Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 3-hydroxyacyl-CoA dehydrogenase type II
B: 3-hydroxyacyl-CoA dehydrogenase type II
C: 3-hydroxyacyl-CoA dehydrogenase type II
D: 3-hydroxyacyl-CoA dehydrogenase type II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,7488
Polymers108,0044
Non-polymers3,7444
Water5,080282
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21040 Å2
ΔGint-116 kcal/mol
Surface area29650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.0, 80.8, 110.0
Angle α, β, γ (deg.)90.0, 105.6, 90.0
Int Tables number5
Space group name H-MC121
DetailsThe biological assembly is the tetramer contained in the asymmetric unit.

-
Components

#1: Protein
3-hydroxyacyl-CoA dehydrogenase type II / Type II HADH / Endoplasmic reticulum-associated amyloid beta-peptide binding protein / Short-chain ...Type II HADH / Endoplasmic reticulum-associated amyloid beta-peptide binding protein / Short-chain type dehydrogenase/reductase XH98G2 / AMYLOID BETA-PEPTIDE-BINDING ALCOHOL DEHYDROGENASE / ABAD


Mass: 27001.072 Da / Num. of mol.: 4 / Mutation: C214R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HADH2, ERAB, XH98G2, SCHAD / Plasmid: PMGH4 / Production host: Escherichia coli (E. coli)
References: UniProt: Q99714, 3-hydroxyacyl-CoA dehydrogenase
#2: Chemical ChemComp-TDT / 1-AZEPAN-1-YL-2-PHENYL-2-(4-THIOXO-1,4-DIHYDRO-PYRAZOLO[3,4-D]PYRIMIDIN-5-YL)ETHANONE ADDUCT


Mass: 1026.861 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C40H44N12O15P2S
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 282 / 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: 2.4 Å3/Da / Density % sol: 49.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6
Details: MME-PEG 2000, sodium citrate, isopropanol, pH 6.0, vapor diffusion, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. all: 69169 / Num. obs: 69169

-
Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
SHELXL-97refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Wild-type human ABAD

Resolution: 2→25 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.263 3429 THIN SHELLS
Rwork0.215 --
all0.215 68595 -
obs0.215 68595 -
Refinement stepCycle: LAST / Resolution: 2→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7224 0 254 282 7760
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.005
X-RAY DIFFRACTIONs_angle_d1.5

+
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