[English] 日本語
Yorodumi
- PDB-4kcx: BRDT in complex with Dinaciclib -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4kcx
TitleBRDT in complex with Dinaciclib
ComponentsBromodomain testis-specific protein
KeywordsCell Cycle/Inhibitor / BRDT / BROMODOMAIN CONTAINING PROTEIN TESTIS SPECIFIC / Cell Cycle-Inhibitor complex
Function / homology
Function and homology information


sperm DNA condensation / male meiotic nuclear division / male meiosis I / regulation of RNA splicing / histone reader activity / RNA splicing / lysine-acetylated histone binding / mRNA processing / histone binding / transcription coactivator activity ...sperm DNA condensation / male meiotic nuclear division / male meiosis I / regulation of RNA splicing / histone reader activity / RNA splicing / lysine-acetylated histone binding / mRNA processing / histone binding / transcription coactivator activity / chromatin remodeling / regulation of DNA-templated transcription / positive regulation of gene expression / nucleus
Similarity search - Function
Bromodomain protein 4, C-terminal / C-terminal domain of bromodomain protein 4 / NET domain superfamily / NET domain profile. / Brdt, bromodomain, repeat II / Brdt, bromodomain, repeat I / NET domain / Bromodomain extra-terminal - transcription regulation / Bromodomain-like / Histone Acetyltransferase; Chain A ...Bromodomain protein 4, C-terminal / C-terminal domain of bromodomain protein 4 / NET domain superfamily / NET domain profile. / Brdt, bromodomain, repeat II / Brdt, bromodomain, repeat I / NET domain / Bromodomain extra-terminal - transcription regulation / Bromodomain-like / Histone Acetyltransferase; Chain A / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-1QK / Bromodomain testis-specific protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMartin, M.P. / Schonbrunn, E.
CitationJournal: Acs Chem.Biol. / Year: 2013
Title: Cyclin-dependent kinase inhibitor dinaciclib interacts with the acetyl-lysine recognition site of bromodomains.
Authors: Martin, M.P. / Olesen, S.H. / Georg, G.I. / Schonbrunn, E.
History
DepositionApr 24, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2013Group: Database references
Revision 1.2Sep 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: Bromodomain testis-specific protein
B: Bromodomain testis-specific protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7275
Polymers27,8962
Non-polymers8303
Water2,468137
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1460 Å2
ΔGint-24 kcal/mol
Surface area11830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.720, 29.950, 71.380
Angle α, β, γ (deg.)90.00, 94.12, 90.00
Int Tables number4
Space group name H-MP1211
DetailsChain A and B form homodimer

-
Components

#1: Protein Bromodomain testis-specific protein / Cancer/testis antigen 9 / CT9 / RING3-like protein


Mass: 13948.153 Da / Num. of mol.: 2 / Fragment: First Bromodomain, UNP residues 21-137
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRDT / Plasmid: PNIC28-BSA4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q58F21
#2: Chemical ChemComp-1QK / 3-[({3-ethyl-5-[(2S)-2-(2-hydroxyethyl)piperidin-1-yl]pyrazolo[1,5-a]pyrimidin-7-yl}amino)methyl]-1-hydroxypyridinium / DINACICLIB / Dinaciclib


Mass: 397.494 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H29N6O2
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 137 / 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: 2.47 Å3/Da / Density % sol: 50.27 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 25mM HEPES PH 7.5, 0.1M NaCl, 1mM DTT 0.1M KSCN, 7% PEG3350, 5% ETGLY, VAPOR DIFFUSION, SITTING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 13, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 18535 / % possible obs: 97 % / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Rmerge(I) obs: 0.127 / Rsym value: 0.127 / Net I/σ(I): 7.7
Reflection shellResolution: 2→2.1 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.624 / Mean I/σ(I) obs: 3.3 / Num. unique all: 2488 / Rsym value: 0.624 / % possible all: 98.1

-
Processing

Software
NameVersionClassification
XDSdata scaling
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4FLP

4flp


Resolution: 2→19.811 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 2 / Phase error: 30.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.253 927 5 %RANDOM
Rwork0.2092 ---
obs0.2114 18535 97.91 %-
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.556 Å2 / ksol: 0.333 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-15.6694 Å2-0 Å2-0.368 Å2
2---12.236 Å2-0 Å2
3----3.4334 Å2
Refinement stepCycle: LAST / Resolution: 2→19.811 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1774 0 59 137 1970
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081889
X-RAY DIFFRACTIONf_angle_d1.1892555
X-RAY DIFFRACTIONf_dihedral_angle_d19.019741
X-RAY DIFFRACTIONf_chiral_restr0.088267
X-RAY DIFFRACTIONf_plane_restr0.005314
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.10530.36731300.3142478X-RAY DIFFRACTION98
2.1053-2.23710.28531320.25782500X-RAY DIFFRACTION99
2.2371-2.40950.30351330.23012523X-RAY DIFFRACTION99
2.4095-2.65150.28591330.2232533X-RAY DIFFRACTION99
2.6515-3.0340.27351330.2152525X-RAY DIFFRACTION98
3.034-3.8180.23851310.18342494X-RAY DIFFRACTION96
3.818-19.81230.20421350.18012555X-RAY DIFFRACTION96
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)
14.82594.0396-1.49114.4417-2.13933.6872-0.12060.10720.4528-0.360.14871.6767-0.2868-0.7237-0.01770.39320.0278-0.12480.243-0.06860.670511.7026-24.98872.5745
23.3581-2.8513-0.87995.15221.1510.85880.01620.22740.1419-0.2603-0.1211-0.0377-0.1394-0.05610.02390.5618-0.0016-0.05360.10430.02180.137332.8827-28.99070.627
36.1663-0.5343-0.75442.5572-0.21593.05060.1232-0.143-0.3879-0.02560.00640.16330.1772-0.0393-0.05660.06180.0752-0.13010.14710.00650.194428.9362-36.25236.8546
43.63091.96650.92481.50841.52622.6103-0.44490.5812-0.4842-1.02520.3010.80180.4821-0.53710.12310.52-0.0472-0.19350.2765-0.03880.553212.9135-36.2043-0.5664
58.31342.6053.58715.74931.44094.00290.05650.0022-0.0545-0.3932-0.25450.77970.1292-0.35220.23660.3824-0.0149-0.00880.1537-0.05710.149719.5772-32.68610.7093
61.1435-1.1584-2.28611.17352.31554.5689-0.0304-0.20290.16350.04160.3931-0.2491-0.24821.0442-0.3660.5987-0.0467-0.03520.2698-0.0440.132532.0026-22.933415.6904
74.44082.2966-1.564.7644-0.95793.99630.38340.18650.61550.0765-0.13821.273-0.5758-0.5057-0.16350.48510.1353-0.04570.2065-0.03610.450714.8342-22.855811.893
86.4968-5.50173.10565.4221-2.76832.7866-0.0332-0.3479-0.56120.6220.05641.49820.128-0.4786-0.20630.7538-0.02350.13330.2497-0.06470.54869.6736-34.124430.1931
95.4922-0.53091.25563.57970.2631.7107-0.024-0.17360.08630.2735-0.04110.4106-0.1485-0.19280.0650.5975-0.0130.11060.1166-0.02990.138521.4265-25.155932.538
102.3498-1.9568-1.45863.04980.03022.52750.0182-0.02170.19110.3784-0.11920.5429-0.0987-0.30910.10070.55820.00880.0570.2158-0.06180.265618.5994-26.419923.1814
110.42060.14721.47830.05150.51715.19350.0061-0.011-0.0381-0.1265-0.1751-0.07320.01930.88720.16580.76480.03360.01520.23210.00670.162731.7218-36.1220.072
124.0737-5.03013.15147.5-2.16974.73290.3314-0.1894-1.0029-0.044-0.10011.20940.4587-0.4475-0.27410.5471-0.09390.01440.1734-0.05450.31213.93-36.36521.2449
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 29:52)
2X-RAY DIFFRACTION2chain 'A' and (resseq 53:65)
3X-RAY DIFFRACTION3chain 'A' and (resseq 66:75)
4X-RAY DIFFRACTION4chain 'A' and (resseq 76:90)
5X-RAY DIFFRACTION5chain 'A' and (resseq 91:108)
6X-RAY DIFFRACTION6chain 'A' and (resseq 109:113)
7X-RAY DIFFRACTION7chain 'A' and (resseq 114:134)
8X-RAY DIFFRACTION8chain 'B' and (resseq 29:52)
9X-RAY DIFFRACTION9chain 'B' and (resseq 53:90)
10X-RAY DIFFRACTION10chain 'B' and (resseq 91:108)
11X-RAY DIFFRACTION11chain 'B' and (resseq 109:113)
12X-RAY DIFFRACTION12chain 'B' and (resseq 114:134)

+
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