General information
PDB ID 5XF5
Title NUCLEOSOME CORE PARTICLE WITH AN ADDUCT OF A BINUCLEAR RAPTA (RU- ARENE-PHOSPHAADAMANTANE) COMPOUND HAVING A 1,2- DIPHENYLETHYLENEDIAMINE LINKER (R,S-CONFIGURATION)
PDB header STRUCTURAL PROTEIN/DNA
Date 2017-04-07
Experimental method X-RAY DIFFRACTION
Resolution (A) 2.82
Kind dna
Organism HOMO SAPIENS
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PDB PDBe MMDB Jena OCA
CATH PDBsum HSSP PDBePISA UniProt
ProteopediA BIPA
Composition of PDB entry and biounits
File: Protein chains: DNA chains: RNA chains: No. of models: Action:
PDB entry:
pdb5xf5.pdb ABCDEFGH IJ 0
Biounits:
5xf5.pdb1.pdb ABCDEFGH IJ 1
Pfam domains
Name: Type: Domain: E-value: Significance: Clan: Prot. chain: Start res.: End res.: Nuc. chains: Int. mode: Action:
Histone Domain P68431_39-132 1.1e-46 1 CL0012 A 38 131 IJ   
CENP-T_C Domain P62805_26-99 4.7e-08 1 CL0012 B 25 98 IJ   
Histone Domain P04908_16-91 4.5e-16 1 CL0012 C 14 90 IJ   
Histone Domain P06899_33-102 5.7e-22 1 CL0012 D 28 98 IJ   
Histone Domain P68431_39-132 1e-46 1 CL0012 E 38 131 IJ   
CENP-T_C Domain P62805_19-99 5.2e-08 1 CL0012 F 20 98 IJ   
Histone Domain P04908_16-91 4.5e-16 1 CL0012 G 14 90 IJ   
Histone Domain P06899_33-102 5.7e-22 1 CL0012 H 28 98 IJ   
Histone_H2A_C Family P04908_92-119 3.1e-18 1 No_clan C 91 119   
Histone_H2A_C Family P04908_92-119 3.1e-18 1 No_clan G 91 119   
SCOP domains
No SCOP domains
GO terms
Protein chains: GO type: GO description:
A/E=1-136 C extracellular exosome
A/E=1-136 C extracellular region
A/E=1-136 C membrane
A/E=1-136 C nuclear chromosome
A/E=1-136 C nuclear nucleosome
A/E=1-136 C nucleoplasm
A/E=1-136 C nucleosome
A/E=1-136 C nucleus
A/E=1-136 C protein-containing complex
A/E=1-136 F cadherin binding
A/E=1-136 F DNA binding
A/E=1-136 F protein heterodimerization activity
A/E=1-136 P blood coagulation
A/E=1-136 P cellular protein metabolic process
A/E=1-136 P chromatin organization
A/E=1-136 P DNA replication-dependent nucleosome assembly
A/E=1-136 P interleukin-7-mediated signaling pathway
A/E=1-136 P negative regulation of gene expression, epigenetic
A/E=1-136 P nucleosome assembly
A/E=1-136 P rDNA heterochromatin assembly
A/E=1-136 P regulation of gene silencing
A/E=1-136 P regulation of gene silencing by miRNA
A/E=1-136 P regulation of megakaryocyte differentiation
A/E=1-136 P telomere organization
B/F=1-103 C extracellular exosome
B/F=1-103 C extracellular region
B/F=1-103 C host cell nucleus
B/F=1-103 C membrane
B/F=1-103 C nuclear chromosome
B/F=1-103 C nuclear chromosome, telomeric region
B/F=1-103 C nuclear nucleosome
B/F=1-103 C nucleoplasm
B/F=1-103 C nucleosome
B/F=1-103 C nucleus
B/F=1-103 C protein-containing complex
B/F=1-103 F DNA binding
B/F=1-103 F protein domain specific binding
B/F=1-103 F protein heterodimerization activity
B/F=1-103 F RNA binding
B/F=1-103 P cellular protein metabolic process
B/F=1-103 P CENP-A containing nucleosome assembly
B/F=1-103 P DNA replication-dependent nucleosome assembly
B/F=1-103 P DNA replication-independent nucleosome assembly
B/F=1-103 P DNA-templated transcription, initiation
B/F=1-103 P double-strand break repair via nonhomologous end joining
B/F=1-103 P negative regulation of gene expression, epigenetic
B/F=1-103 P negative regulation of megakaryocyte differentiation
B/F=1-103 P nucleosome assembly
B/F=1-103 P rDNA heterochromatin assembly
B/F=1-103 P regulation of gene silencing by miRNA
B/F=1-103 P regulation of megakaryocyte differentiation
B/F=1-103 P telomere capping
B/F=1-103 P telomere organization
C/G=1-130 C extracellular exosome
C/G=1-130 C nuclear chromatin
C/G=1-130 C nucleosome
C/G=1-130 C nucleus
C/G=1-130 F DNA binding
C/G=1-130 F protein heterodimerization activity
C/G=1-130 P chromatin organization
C/G=1-130 P chromatin silencing
C/G=1-130 P negative regulation of cell population proliferation
D/H=1-126 C cytosol
D/H=1-126 C extracellular space
D/H=1-126 C nucleoplasm
D/H=1-126 C nucleosome
D/H=1-126 C nucleus
D/H=1-126 F DNA binding
D/H=1-126 F lipopolysaccharide binding
D/H=1-126 F protein heterodimerization activity
D/H=1-126 P antibacterial humoral response
D/H=1-126 P antimicrobial humoral immune response mediated by antimicrobial peptide
D/H=1-126 P defense response to Gram-negative bacterium
D/H=1-126 P defense response to Gram-positive bacterium
D/H=1-126 P innate immune response in mucosa
D/H=1-126 P killing of cells of other organism
D/H=1-126 P negative regulation of tumor necrosis factor-mediated signaling pathway
D/H=1-126 P nucleosome assembly
D/H=1-126 P protein ubiquitination
Sequences
Download file with secondary structure created by Stride  
5xf5.pdb1.pdb:   [ download sequences in FASTA format ]
I (dna): 
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J (dna): 
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A (protein): 
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B (protein): 
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C (protein): 
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D (protein): 
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E (protein): 
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F (protein): 
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G (protein): 
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H (protein): 
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