NPIDB: 5CPI structure

General information

PDB ID

5CPI

Title

NUCLEOSOME CONTAINING UNMETHYLATED SAT2R DNA

PDB header

STRUCTURAL PROTEIN/DNA

Date

2015-07-21

Experimental method

X-RAY DIFFRACTION

Resolution (A)

2.9

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:

pdb5cpi.pdb	ABCDEFGH	IJ		0

Biounits:

5cpi.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	1e-46	1	CL0012	A	38	131	IJ	H-Bb H-Mj S-Bb L-Bb
CENP-T_C	Domain	P62805_26-99	4.2e-08	1	CL0012	B	26	98	IJ	H-Bb S-Bb L-Bb
Histone	Domain	P04908_16-91	2.4e-16	1	CL0012	C	11	90	IJ	H-Bb S-Bb L-Bb L-Mn
Histone	Domain	P06899_33-102	9.4e-22	1	CL0012	D	32	101	IJ	H-Bb S-Bb L-Bb L-Mn
Histone	Domain	P68431_39-132	1.1e-46	1	CL0012	E	38	131	IJ	H-Bb S-Bb L-Bb
CENP-T_C	Domain	P62805_19-99	4.9e-08	1	CL0012	F	25	98	IJ	H-Bb S-Bb L-Bb
Histone	Domain	P04908_16-91	4.8e-16	1	CL0012	G	15	90	IJ	H-Bb S-Bb L-Bb
Histone	Domain	P06899_33-102	1.4e-21	1	CL0012	H	33	101	IJ	H-Bb L-Bb
Histone_H2A_C	Family	P04908_92-119	2.5e-17	1	No_clan	C	91	118
Histone_H2A_C	Family	P04908_92-119	2.3e-17	1	No_clan	G	91	118

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

5cpi.pdb1.pdb: [ download sequences in FASTA format ]

I (dna):