[English] 日本語
Yorodumi
- PDB-5l7y: 17beta-hydroxysteroid dehydrogenase 14 variant T205 in complex wi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5l7y
Title17beta-hydroxysteroid dehydrogenase 14 variant T205 in complex with a non-steroidal inhibitor.
Components17-beta-hydroxysteroid dehydrogenase 14
KeywordsOXIDOREDUCTASE / hydroxysteroid dehydrogenase / inhibitor complex
Function / homology
Function and homology information


D-threo-aldose 1-dehydrogenase / D-threo-aldose 1-dehydrogenase activity / Estrogen biosynthesis / L-fucose catabolic process / estradiol 17-beta-dehydrogenase [NAD(P)+] activity / steroid catabolic process / identical protein binding / cytosol
Similarity search - Function
Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Enoyl-(Acyl carrier protein) reductase / 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
Chem-6QO / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / L-fucose dehydrogenase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.912 Å
AuthorsBertoletti, N. / Braun, F. / Marchais-Oberwinkler, S. / Heine, A. / Klebe, G.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research FoundationKL-1204/15-1 Germany
German Research FoundationMA-5287/1-1 Germany
CitationJournal: J. Med. Chem. / Year: 2016
Title: First Structure-Activity Relationship of 17 beta-Hydroxysteroid Dehydrogenase Type 14 Nonsteroidal Inhibitors and Crystal Structures in Complex with the Enzyme.
Authors: Braun, F. / Bertoletti, N. / Moller, G. / Adamski, J. / Steinmetzer, T. / Salah, M. / Abdelsamie, A.S. / van Koppen, C.J. / Heine, A. / Klebe, G. / Marchais-Oberwinkler, S.
History
DepositionJun 4, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 21, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Author supporting evidence / Data collection / Category: diffrn_source / pdbx_audit_support
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_audit_support.funding_organization
Revision 1.2Jan 10, 2024Group: 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 17-beta-hydroxysteroid dehydrogenase 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0245
Polymers28,6831
Non-polymers1,3414
Water3,387188
1
A: 17-beta-hydroxysteroid dehydrogenase 14
hetero molecules

A: 17-beta-hydroxysteroid dehydrogenase 14
hetero molecules

A: 17-beta-hydroxysteroid dehydrogenase 14
hetero molecules

A: 17-beta-hydroxysteroid dehydrogenase 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,09520
Polymers114,7314
Non-polymers5,36416
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
crystal symmetry operation5_455-x-1,y,-z1
crystal symmetry operation6_555x,-y,-z1
Buried area21200 Å2
ΔGint-192 kcal/mol
Surface area32010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.571, 91.571, 132.518
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-469-

HOH

21A-580-

HOH

31A-588-

HOH

-
Components

#1: Protein 17-beta-hydroxysteroid dehydrogenase 14 / 17-beta-HSD 14 / 17-beta-hydroxysteroid dehydrogenase DHRS10 / Dehydrogenase/reductase SDR family ...17-beta-HSD 14 / 17-beta-hydroxysteroid dehydrogenase DHRS10 / Dehydrogenase/reductase SDR family member 10 / Retinal short-chain dehydrogenase/reductase retSDR3 / Short chain dehydrogenase/reductase family 47C member 1


Mass: 28682.740 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HSD17B14, DHRS10, SDR3, SDR47C1, UNQ502/PRO474 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS
References: UniProt: Q9BPX1, Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-6QO / (4-fluoranyl-3-oxidanyl-phenyl)-[6-(2-fluoranyl-3-oxidanyl-phenyl)pyridin-2-yl]methanone


Mass: 327.282 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H11F2NO3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 188 / 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: 2.43 Å3/Da / Density % sol: 49.33 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: CHES 0.1 M pH 9.50 tri-sodium-citrate 1.00 M DMSO 5%
PH range: 8-9.50

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.7999 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 6, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7999 Å / Relative weight: 1
ReflectionResolution: 1.91→50 Å / Num. obs: 21943 / % possible obs: 98.9 % / Redundancy: 7.17 % / Rsym value: 0.088 / Net I/σ(I): 16.75
Reflection shellResolution: 1.91→2.03 Å / Redundancy: 6.66 % / Rmerge(I) obs: 0.497 / Mean I/σ(I) obs: 3.71 / % possible all: 94.8

-
Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: 000)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5EN4

5en4


Resolution: 1.912→46.31 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 14.82
RfactorNum. reflection% reflection
Rfree0.1645 1098 5 %
Rwork0.1379 --
obs0.1393 21940 98.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.912→46.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1857 0 93 188 2138
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091997
X-RAY DIFFRACTIONf_angle_d0.9932729
X-RAY DIFFRACTIONf_dihedral_angle_d19.9871178
X-RAY DIFFRACTIONf_chiral_restr0.06311
X-RAY DIFFRACTIONf_plane_restr0.006373
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9121-1.99910.21551270.18192408X-RAY DIFFRACTION93
1.9991-2.10450.19351360.15582588X-RAY DIFFRACTION100
2.1045-2.23640.16761370.13472601X-RAY DIFFRACTION100
2.2364-2.4090.17581370.13322596X-RAY DIFFRACTION100
2.409-2.65140.19161370.13342612X-RAY DIFFRACTION100
2.6514-3.0350.16491380.13982615X-RAY DIFFRACTION100
3.035-3.82360.15921400.13542654X-RAY DIFFRACTION100
3.8236-46.32320.13871460.13122768X-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