[English] 日本語
Yorodumi
- PDB-5enc: Crystal structure of the second bromodomain of Pleckstrin homolog... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5enc
TitleCrystal structure of the second bromodomain of Pleckstrin homology domain interacting protein (PHIP) in complex with N-(2,6-Dichlorobenzyl)acetamide (SGC - Diamond I04-1 fragment screening)
ComponentsPH-interacting protein
KeywordsSIGNALING PROTEIN / bromodomain / PHIP / crystallographic fragment screen / Structural Genomics / Structural Genomics Consortium / SGC / transcription
Function / homology
Function and homology information


regulation of cell morphogenesis / positive regulation of insulin-like growth factor receptor signaling pathway / RHOBTB2 GTPase cycle / cytoskeleton organization / positive regulation of mitotic nuclear division / negative regulation of extrinsic apoptotic signaling pathway / regulation of protein phosphorylation / insulin receptor binding / lysine-acetylated histone binding / insulin receptor signaling pathway ...regulation of cell morphogenesis / positive regulation of insulin-like growth factor receptor signaling pathway / RHOBTB2 GTPase cycle / cytoskeleton organization / positive regulation of mitotic nuclear division / negative regulation of extrinsic apoptotic signaling pathway / regulation of protein phosphorylation / insulin receptor binding / lysine-acetylated histone binding / insulin receptor signaling pathway / regulation of cell shape / positive regulation of cell population proliferation / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / nucleus
Similarity search - Function
: / Bromodomain-like / Histone Acetyltransferase; Chain A / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily ...: / Bromodomain-like / Histone Acetyltransferase; Chain A / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
~{N}-[[2,6-bis(chloranyl)phenyl]methyl]ethanamide / PH-interacting protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.59 Å
AuthorsKrojer, T. / Talon, R. / Collins, P. / Bradley, A. / Cox, O. / Szykowska, A. / Burgess-Brown, N. / Brennan, P. / Bountra, C. / Arrowsmith, C.H. ...Krojer, T. / Talon, R. / Collins, P. / Bradley, A. / Cox, O. / Szykowska, A. / Burgess-Brown, N. / Brennan, P. / Bountra, C. / Arrowsmith, C.H. / Edwards, A. / von Delft, F. / Structural Genomics Consortium (SGC)
CitationJournal: Chem Sci / Year: 2016
Title: A poised fragment library enables rapid synthetic expansion yielding the first reported inhibitors of PHIP(2), an atypical bromodomain.
Authors: Cox, O.B. / Krojer, T. / Collins, P. / Monteiro, O. / Talon, R. / Bradley, A. / Fedorov, O. / Amin, J. / Marsden, B.D. / Spencer, J. / von Delft, F. / Brennan, P.E.
History
DepositionNov 9, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 27, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 11, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI ..._citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PH-interacting protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9374
Polymers15,5951
Non-polymers3423
Water3,243180
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area400 Å2
ΔGint5 kcal/mol
Surface area8220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.687, 91.582, 24.033
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein PH-interacting protein / PHIP / IRS-1 PH domain-binding protein / WD repeat-containing protein 11


Mass: 15594.661 Da / Num. of mol.: 1 / Fragment: Bromodomain, UNP residues 1315-1440
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PHIP, WDR11 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8WWQ0
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-5QD / ~{N}-[[2,6-bis(chloranyl)phenyl]methyl]ethanamide


Mass: 218.080 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H9Cl2NO
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 180 / 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: 2.14 Å3/Da / Density % sol: 42.56 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M HEPES pH 7.5 , 0.15M magnesium chloride , 32% PEG3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92001 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 17, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92001 Å / Relative weight: 1
ReflectionResolution: 1.59→28.8 Å / Num. obs: 18820 / % possible obs: 99.8 % / Redundancy: 6.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.041 / Rpim(I) all: 0.018 / Net I/σ(I): 21.8 / Num. measured all: 120066
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
1.59-1.636.20.7262.4833913430.7910.31498.7
7.11-28.85.50.03653.114412640.9990.01798.2

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
Aimless0.3.11data scaling
REFMAC5.8.0131refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3MB3

3mb3


Resolution: 1.59→28.8 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.94 / SU B: 4.491 / SU ML: 0.081 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.101 / ESU R Free: 0.105 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2466 933 5 %RANDOM
Rwork0.2035 ---
obs0.2057 17845 99.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 65.92 Å2 / Biso mean: 31.014 Å2 / Biso min: 19.06 Å2
Baniso -1Baniso -2Baniso -3
1--1.16 Å2-0 Å20 Å2
2--1.65 Å2-0 Å2
3----0.5 Å2
Refinement stepCycle: final / Resolution: 1.59→28.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1018 0 21 180 1219
Biso mean--44.18 40.34 -
Num. residues----124
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0191070
X-RAY DIFFRACTIONr_bond_other_d0.0020.02978
X-RAY DIFFRACTIONr_angle_refined_deg1.6621.9591440
X-RAY DIFFRACTIONr_angle_other_deg1.02432258
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2375125
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.79623.63655
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.98215188
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.797159
X-RAY DIFFRACTIONr_chiral_restr0.1070.2149
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211237
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02252
X-RAY DIFFRACTIONr_mcbond_it1.342.074500
X-RAY DIFFRACTIONr_mcbond_other1.3392.076501
X-RAY DIFFRACTIONr_mcangle_it2.0863.109628
LS refinement shellResolution: 1.589→1.631 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.396 52 -
Rwork0.269 1290 -
all-1342 -
obs--98.82 %
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)Origin x (Å)Origin y (Å)Origin z (Å)
11.88893.5208-1.64797.4994-3.6461.790.0253-0.1026-0.13620.1162-0.1726-0.3039-0.06180.07550.14730.052-0.03580.01140.0438-0.0260.12028.618620.4281-11.3141
23.16720.6544-0.30380.16790.10011.01660.0802-0.14420.23370.005-0.02420.023-0.02930.0107-0.0560.0881-0.0214-0.01320.0147-0.02620.1151-6.529716.982-5.3996
31.52780.5782-0.0793.34541.22090.5045-0.1574-0.17480.02980.25310.06880.24110.13490.06140.08870.1124-0.03820.01070.10130.01750.02-22.26762.0986-5.5145
41.93121.00920.55070.54330.40051.321-0.05090.1058-0.11230.00790.0403-0.0740.1886-0.1840.01070.1213-0.0256-0.04080.0489-0.02990.0854-10.35095.6451-10.5925
53.52191.4299-0.41360.70220.10990.7109-0.04370.23530.1641-0.03080.06390.0425-0.0089-0.1057-0.02010.057-0.0248-0.00080.03730.02820.1275-10.438715.0864-16.7983
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1313 - 1319
2X-RAY DIFFRACTION2A1320 - 1334
3X-RAY DIFFRACTION3A1335 - 1356
4X-RAY DIFFRACTION4A1357 - 1395
5X-RAY DIFFRACTION5A1396 - 1436

+
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://pdbjlc1.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