[English] 日本語
Yorodumi
- PDB-4yyz: 11B-HYDROXYSTEROID DEHYDROGENASE TYPE I IN COMPLEX WITH INHIBITOR -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4yyz
Title11B-HYDROXYSTEROID DEHYDROGENASE TYPE I IN COMPLEX WITH INHIBITOR
ComponentsCorticosteroid 11-beta-dehydrogenase isozyme 1
KeywordsOXIDOREDUCTASE / DEHYDROGENASE INHIBITOR / BHSD
Function / homology
Function and homology information


11beta-hydroxysteroid dehydrogenase / 11-beta-hydroxysteroid dehydrogenase (NADP+) activity / cortisol dehydrogenase activity / 7beta-hydroxysteroid dehydrogenase (NADP+) / 7-beta-hydroxysteroid dehydrogenase (NADP+) activity / Glucocorticoid biosynthesis / steroid catabolic process / Prednisone ADME / steroid binding / lung development ...11beta-hydroxysteroid dehydrogenase / 11-beta-hydroxysteroid dehydrogenase (NADP+) activity / cortisol dehydrogenase activity / 7beta-hydroxysteroid dehydrogenase (NADP+) / 7-beta-hydroxysteroid dehydrogenase (NADP+) activity / Glucocorticoid biosynthesis / steroid catabolic process / Prednisone ADME / steroid binding / lung development / NADP binding / intracellular membrane-bounded organelle / endoplasmic reticulum membrane / protein homodimerization activity / membrane
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
Chem-4JX / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 11-beta-hydroxysteroid dehydrogenase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsBranden, G. / Boden, C. / Ogg, D.
CitationJournal: Medchemcomm / Year: 2016
Title: Design of pyrozolo-pyrimidines as 11beta-HSD1 inhibitors through optimisation of molecular electrostatic potential.
Authors: Robb, G.R. / Boyd, S. / Davies, C.D. / Dossiter, A.G. / Goldberg, F.W. / Kemmitt, P.D. / Scott, J.S. / Swales, J.G.
History
DepositionMar 24, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Feb 3, 2016Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Corticosteroid 11-beta-dehydrogenase isozyme 1
B: Corticosteroid 11-beta-dehydrogenase isozyme 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,9366
Polymers56,7682
Non-polymers2,1684
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7420 Å2
ΔGint-59 kcal/mol
Surface area20180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.788, 107.788, 136.020
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

-
Components

#1: Protein Corticosteroid 11-beta-dehydrogenase isozyme 1 / 11-beta-hydroxysteroid dehydrogenase 1 / 11-beta-HSD1


Mass: 28383.988 Da / Num. of mol.: 2 / Fragment: UNP residues 26-284
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HSD11B1, HSD11, HSD11L
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P28845, 11beta-hydroxysteroid dehydrogenase
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical ChemComp-4JX / N-[(1R,2s,3S,5s,7s)-5-hydroxytricyclo[3.3.1.1~3,7~]dec-2-yl]-5,7-dimethylpyrazolo[1,5-a]pyrimidine-3-carboxamide


Mass: 340.419 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H24N4O2

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.03 Å3/Da / Density % sol: 69.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 20mM HEPES, 100mM NaCl, 2mM TCEP, 10uM NADP / PH range: 8

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.939 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 13, 2010
RadiationMonochromator: Double crystal, Si(111) or Si(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.939 Å / Relative weight: 1
ReflectionResolution: 3.15→46.67 Å / Num. obs: 15792 / % possible obs: 97.3 % / Redundancy: 3.4 % / Biso Wilson estimate: 109.67 Å2 / Rmerge(I) obs: 0.113 / Net I/σ(I): 6.3
Reflection shellResolution: 3.15→3.23 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.507 / Mean I/σ(I) obs: 1.7 / % possible all: 99.6

-
Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
BUSTER2.11.6refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→19.75 Å / Cor.coef. Fo:Fc: 0.9149 / Cor.coef. Fo:Fc free: 0.8787 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.441
RfactorNum. reflection% reflectionSelection details
Rfree0.2672 751 5 %RANDOM
Rwork0.2181 ---
obs0.2204 15023 97.1 %-
Displacement parametersBiso mean: 139.34 Å2
Baniso -1Baniso -2Baniso -3
1--15.1642 Å20 Å20 Å2
2---15.1642 Å20 Å2
3---30.3284 Å2
Refine analyzeLuzzati coordinate error obs: 0.416 Å
Refinement stepCycle: LAST / Resolution: 3.2→19.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3960 0 146 0 4106
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014291HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.245914HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1519SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes76HARMONIC2
X-RAY DIFFRACTIONt_gen_planes700HARMONIC5
X-RAY DIFFRACTIONt_it4291HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.88
X-RAY DIFFRACTIONt_other_torsion22.96
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion560SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5362SEMIHARMONIC4
LS refinement shellResolution: 3.2→3.42 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.3495 162 5.92 %
Rwork0.3173 2575 -
all0.3193 2737 -
obs--99.46 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)DetailsOrigin x (Å)Origin y (Å)Origin z (Å)
14.5455-1.12810.34893.0116-0.76599.13420.2978-0.2029-0.387-0.22140.1132-0.2960.59762.2305-0.411-0.5903-0.1997-0.07020.6758-0.1745-0.2358Chain A51.3505-43.784520.335
23.17080.94530.61292.9701-0.52826.88160.20630.25740.6738-0.0980.33740.3554-1.92240.0641-0.54370.1788-0.45270.2348-0.15610.0982-0.198Chain B33.6269-21.44599.4294
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ B|* }
2X-RAY DIFFRACTION2{ B|* }

+
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