[English] 日本語
Yorodumi
- PDB-9zxm: DDB1 delta with compound 6 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9zxm
TitleDDB1 delta with compound 6
ComponentsDNA damage-binding protein 1
KeywordsLIGASE / E3 Ligase / DNA-encoded library
Function / homology
Function and homology information


positive regulation by virus of viral protein levels in host cell / spindle assembly involved in female meiosis / epigenetic programming in the zygotic pronuclei / UV-damage excision repair / biological process involved in interaction with symbiont / regulation of mitotic cell cycle phase transition / WD40-repeat domain binding / Cul4A-RING E3 ubiquitin ligase complex / Cul4-RING E3 ubiquitin ligase complex / Cul4B-RING E3 ubiquitin ligase complex ...positive regulation by virus of viral protein levels in host cell / spindle assembly involved in female meiosis / epigenetic programming in the zygotic pronuclei / UV-damage excision repair / biological process involved in interaction with symbiont / regulation of mitotic cell cycle phase transition / WD40-repeat domain binding / Cul4A-RING E3 ubiquitin ligase complex / Cul4-RING E3 ubiquitin ligase complex / Cul4B-RING E3 ubiquitin ligase complex / ubiquitin ligase complex scaffold activity / negative regulation of reproductive process / negative regulation of developmental process / viral release from host cell / cullin family protein binding / ectopic germ cell programmed cell death / positive regulation of viral genome replication / proteasomal protein catabolic process / positive regulation of gluconeogenesis / nucleotide-excision repair / sperm end piece / Recognition of DNA damage by PCNA-containing replication complex / regulation of circadian rhythm / DNA Damage Recognition in GG-NER / Dual Incision in GG-NER / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / Wnt signaling pathway / Formation of Incision Complex in GG-NER / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / positive regulation of protein catabolic process / cellular response to UV / rhythmic process / site of double-strand break / sperm principal piece / Neddylation / sperm midpiece / ubiquitin-dependent protein catabolic process / damaged DNA binding / proteasome-mediated ubiquitin-dependent protein catabolic process / protein-macromolecule adaptor activity / chromosome, telomeric region / protein ubiquitination / DNA repair / apoptotic process / DNA damage response / negative regulation of apoptotic process / protein-containing complex binding / nucleolus / protein-containing complex / : / DNA binding / extracellular exosome / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
: / RSE1/DDB1/CPSF1 second beta-propeller / Cleavage/polyadenylation specificity factor, A subunit, C-terminal / Cleavage/polyadenylation specificity factor, A subunit, N-terminal / : / CPSF A subunit region / RSE1/DDB1/CPSF1 first beta-propeller / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
: / DNA damage-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.195 Å
AuthorsDigianantonio, K.M. / Karim, M.F. / Bekes, M.
Funding support United States, 1items
OrganizationGrant numberCountry
Other private United States
CitationJournal: Acs Med.Chem.Lett. / Year: 2026
Title: DNA-Encoded Library (DEL) Selection Identifies a Distinct DDB1 Ligand Binding Site
Authors: Reddy Guduru, S.K. / Caldwell, J.P. / Digianantonio, K.M. / Prophet, S.M. / Yang, S. / Gareiss, P. / Jones, C. / Harbin, A. / Driscoll, B. / Karim, M.F. / Scott, A. / Patel, A. / Chapman, A. ...Authors: Reddy Guduru, S.K. / Caldwell, J.P. / Digianantonio, K.M. / Prophet, S.M. / Yang, S. / Gareiss, P. / Jones, C. / Harbin, A. / Driscoll, B. / Karim, M.F. / Scott, A. / Patel, A. / Chapman, A.E. / Crandall, M. / Miklossy, G. / Barczak, N.T. / Stroppa, A.P. / Corradi, J.P. / Clark, J.J. / Chung, M.K. / Reinhardt, N.R. / Butcher, W.E. / Wilson, R. / Stiff, C. / Fathizadeh, A. / Yuan, L. / Wang, G. / Dong, H. / Beno, B.R. / Zimmermann, K. / Langley, D.R. / Cacace, A.M. / Bekes, M.
History
DepositionJan 5, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2026Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA damage-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,5875
Polymers95,7741
Non-polymers8134
Water3,279182
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.755, 115.924, 120.374
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein DNA damage-binding protein 1 / DDB p127 subunit / DNA damage-binding protein a / DDBa / Damage-specific DNA-binding protein 1 / ...DDB p127 subunit / DNA damage-binding protein a / DDBa / Damage-specific DNA-binding protein 1 / HBV X-associated protein 1 / XAP-1 / UV-damaged DNA-binding factor / UV-damaged DNA-binding protein 1 / UV-DDB 1 / XPE-binding factor / XPE-BF / Xeroderma pigmentosum group E-complementing protein / XPCe


Mass: 95773.695 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DDB1, XAP1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q16531
#2: Chemical ChemComp-A1C4E / (3S,5S)-1-{(4P)-4-(2,2-difluoro-2H-1,3-benzodioxol-4-yl)-3-[(propan-2-yl)oxy]benzene-1-carbonyl}-N-methyl-5-phenylpiperidine-3-carboxamide


Mass: 536.566 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H30F2N2O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 182 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.47 Å3/Da / Density % sol: 50.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2M ammonium acetate, 0.1M Bis Tris pH 5.5-6.5, and 25% PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.9201 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 13, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9201 Å / Relative weight: 1
ReflectionResolution: 2.195→33.11 Å / Num. obs: 48885 / % possible obs: 99.16 % / Redundancy: 7.4 % / Biso Wilson estimate: 28.06 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.1782 / Rpim(I) all: 0.07023 / Rrim(I) all: 0.1919 / Net I/σ(I): 8.05
Reflection shellResolution: 2.2→2.22 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.7913 / Mean I/σ(I) obs: 1.56 / Num. unique obs: 1306 / CC1/2: 0.584 / CC star: 0.859 / Rpim(I) all: 0.3306 / Rrim(I) all: 0.8588 / % possible all: 95.28

-
Processing

Software
NameVersionClassification
REFMAC5.8.0430 (refmacat 0.4.105)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.195→33.11 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.919 / SU B: 7.19 / SU ML: 0.175 / Cross valid method: THROUGHOUT / ESU R: 0.241 / ESU R Free: 0.206
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2461 2406 4.924 %RANDOM
Rwork0.1911 46459 --
all0.194 ---
obs-48865 99.353 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 38.786 Å2
Baniso -1Baniso -2Baniso -3
1--0.574 Å20 Å20 Å2
2--1.957 Å2-0 Å2
3----1.382 Å2
Refinement stepCycle: LAST / Resolution: 2.195→33.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6237 0 57 182 6476
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0126442
X-RAY DIFFRACTIONr_bond_other_d0.0010.0166103
X-RAY DIFFRACTIONr_angle_refined_deg1.5751.838730
X-RAY DIFFRACTIONr_angle_other_deg0.5351.75114065
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6265808
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.771533
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.589101110
X-RAY DIFFRACTIONr_dihedral_angle_6_deg13.96210286
X-RAY DIFFRACTIONr_chiral_restr0.0750.21000
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027520
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021438
X-RAY DIFFRACTIONr_nbd_refined0.1980.2956
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2130.25611
X-RAY DIFFRACTIONr_nbtor_refined0.1760.23026
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0890.23477
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1730.2266
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2310.240
X-RAY DIFFRACTIONr_nbd_other0.2840.282
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2850.27
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1020.21
X-RAY DIFFRACTIONr_mcbond_it3.1423.7133223
X-RAY DIFFRACTIONr_mcbond_other3.1413.7133223
X-RAY DIFFRACTIONr_mcangle_it5.0576.6474025
X-RAY DIFFRACTIONr_mcangle_other5.0566.6474026
X-RAY DIFFRACTIONr_scbond_it3.7384.133219
X-RAY DIFFRACTIONr_scbond_other3.7374.133220
X-RAY DIFFRACTIONr_scangle_it6.047.4134702
X-RAY DIFFRACTIONr_scangle_other6.047.4134703
X-RAY DIFFRACTIONr_lrange_it8.82141.4436657
X-RAY DIFFRACTIONr_lrange_other8.81941.5136626
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.195-2.2520.3131460.28931460.2935700.9230.92792.21290.285
2.252-2.3140.3141890.27732900.27934790.9160.9341000.268
2.314-2.380.2941820.25831840.2633660.9280.9451000.245
2.38-2.4530.2981540.24731640.24933180.930.9511000.233
2.453-2.5330.2631420.24630470.24731890.9420.9541000.233
2.533-2.6210.2531480.22529540.22631020.9490.9621000.206
2.621-2.720.2861720.20428220.20929940.9460.971000.181
2.72-2.830.2731510.19827500.20129010.9530.9741000.175
2.83-2.9550.2371340.18226150.18427490.9630.9781000.16
2.955-3.0980.251180.17625510.17926690.9580.9791000.153
3.098-3.2640.2251050.17424200.17625250.9640.9811000.155
3.264-3.460.231040.17122940.17423980.9650.9821000.155
3.46-3.6960.2561140.17421560.17822700.960.9811000.16
3.696-3.9880.231130.16720210.17121350.9670.98299.95320.154
3.988-4.3620.1831120.15518320.15719440.980.9851000.145
4.362-4.8660.203940.13717040.14117980.9760.9881000.133
4.866-5.5990.21910.16715070.16915980.9770.9841000.158
5.599-6.8090.237630.18713020.18913650.9760.9831000.175
6.809-9.4320.299420.19110560.19510980.950.9781000.183
9.432-33.110.3320.2096440.2146960.9460.97497.12640.217

+
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