Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

5DF5

The structure of oxidized rat cytochrome c (T28E) at 1.30 angstroms resolution.

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0002931	biological_process	response to ischemia
A	0005634	cellular_component	nucleus
A	0005739	cellular_component	mitochondrion
A	0005758	cellular_component	mitochondrial intermembrane space
A	0005829	cellular_component	cytosol
A	0006122	biological_process	mitochondrial electron transport, ubiquinol to cytochrome c
A	0006123	biological_process	mitochondrial electron transport, cytochrome c to oxygen
A	0006915	biological_process	apoptotic process
A	0006979	biological_process	response to oxidative stress
A	0009055	molecular_function	electron transfer activity
A	0009629	biological_process	response to gravity
A	0010730	biological_process	negative regulation of hydrogen peroxide biosynthetic process
A	0010996	biological_process	response to auditory stimulus
A	0019899	molecular_function	enzyme binding
A	0020037	molecular_function	heme binding
A	0022904	biological_process	respiratory electron transport chain
A	0034349	biological_process	glial cell apoptotic process
A	0034465	biological_process	response to carbon monoxide
A	0042743	biological_process	hydrogen peroxide metabolic process
A	0043293	cellular_component	apoptosome
A	0046688	biological_process	response to copper ion
A	0046872	molecular_function	metal ion binding
A	1901857	biological_process	positive regulation of cellular respiration
B	0002931	biological_process	response to ischemia
B	0005634	cellular_component	nucleus
B	0005739	cellular_component	mitochondrion
B	0005758	cellular_component	mitochondrial intermembrane space
B	0005829	cellular_component	cytosol
B	0006122	biological_process	mitochondrial electron transport, ubiquinol to cytochrome c
B	0006123	biological_process	mitochondrial electron transport, cytochrome c to oxygen
B	0006915	biological_process	apoptotic process
B	0006979	biological_process	response to oxidative stress
B	0009055	molecular_function	electron transfer activity
B	0009629	biological_process	response to gravity
B	0010730	biological_process	negative regulation of hydrogen peroxide biosynthetic process
B	0010996	biological_process	response to auditory stimulus
B	0019899	molecular_function	enzyme binding
B	0020037	molecular_function	heme binding
B	0022904	biological_process	respiratory electron transport chain
B	0034349	biological_process	glial cell apoptotic process
B	0034465	biological_process	response to carbon monoxide
B	0042743	biological_process	hydrogen peroxide metabolic process
B	0043293	cellular_component	apoptosome
B	0046688	biological_process	response to copper ion
B	0046872	molecular_function	metal ion binding
B	1901857	biological_process	positive regulation of cellular respiration
C	0002931	biological_process	response to ischemia
C	0005634	cellular_component	nucleus
C	0005739	cellular_component	mitochondrion
C	0005758	cellular_component	mitochondrial intermembrane space
C	0005829	cellular_component	cytosol
C	0006122	biological_process	mitochondrial electron transport, ubiquinol to cytochrome c
C	0006123	biological_process	mitochondrial electron transport, cytochrome c to oxygen
C	0006915	biological_process	apoptotic process
C	0006979	biological_process	response to oxidative stress
C	0009055	molecular_function	electron transfer activity
C	0009629	biological_process	response to gravity
C	0010730	biological_process	negative regulation of hydrogen peroxide biosynthetic process
C	0010996	biological_process	response to auditory stimulus
C	0019899	molecular_function	enzyme binding
C	0020037	molecular_function	heme binding
C	0022904	biological_process	respiratory electron transport chain
C	0034349	biological_process	glial cell apoptotic process
C	0034465	biological_process	response to carbon monoxide
C	0042743	biological_process	hydrogen peroxide metabolic process
C	0043293	cellular_component	apoptosome
C	0046688	biological_process	response to copper ion
C	0046872	molecular_function	metal ion binding
C	1901857	biological_process	positive regulation of cellular respiration
D	0002931	biological_process	response to ischemia
D	0005634	cellular_component	nucleus
D	0005739	cellular_component	mitochondrion
D	0005758	cellular_component	mitochondrial intermembrane space
D	0005829	cellular_component	cytosol
D	0006122	biological_process	mitochondrial electron transport, ubiquinol to cytochrome c
D	0006123	biological_process	mitochondrial electron transport, cytochrome c to oxygen
D	0006915	biological_process	apoptotic process
D	0006979	biological_process	response to oxidative stress
D	0009055	molecular_function	electron transfer activity
D	0009629	biological_process	response to gravity
D	0010730	biological_process	negative regulation of hydrogen peroxide biosynthetic process
D	0010996	biological_process	response to auditory stimulus
D	0019899	molecular_function	enzyme binding
D	0020037	molecular_function	heme binding
D	0022904	biological_process	respiratory electron transport chain
D	0034349	biological_process	glial cell apoptotic process
D	0034465	biological_process	response to carbon monoxide
D	0042743	biological_process	hydrogen peroxide metabolic process
D	0043293	cellular_component	apoptosome
D	0046688	biological_process	response to copper ion
D	0046872	molecular_function	metal ion binding
D	1901857	biological_process	positive regulation of cellular respiration

Functional Information from PDB Data

site_id	AC1
Number of Residues	20
Details	binding site for residue HEC A 201

Chain	Residue
A	LYS13
A	TYR48
A	THR49
A	ASN52
A	TRP59
A	TYR67
A	THR78
A	LYS79
A	MET80
A	ILE81
A	PHE82
A	CYS14
A	HOH318
A	CYS17
A	HIS18
A	GLU28
A	GLY29
A	PRO30
A	THR40
A	GLY41

site_id	AC2
Number of Residues	8
Details	binding site for residue FC6 B 202

Chain	Residue
A	LYS87
A	LYS88
A	GLY89
A	GLU90
B	LYS87
B	LYS88
B	GLY89
B	GLU90

site_id	AC3
Number of Residues	10
Details	binding site for residue FC6 B 203

Chain	Residue
B	ASP2
B	GLU4
B	LYS8
B	LYS39
B	GLY56
B	THR58
B	HOH329
B	HOH373
D	ILE57
D	THR58

site_id	AC4
Number of Residues	7
Details	binding site for residue FC6 C 202

Chain	Residue
C	LYS87
C	LYS88
C	GLY89
D	LYS87
D	LYS88
D	GLY89
D	HOH364

site_id	AC5
Number of Residues	23
Details	binding site for Di-peptide HEC B 201 and CYS B 14

Chain	Residue
B	PHE10
B	LYS13
B	ALA15
B	GLN16
B	CYS17
B	HIS18
B	GLU28
B	GLY29
B	PRO30
B	THR40
B	GLY41
B	TYR48
B	THR49
B	ASN52
B	TRP59
B	TYR67
B	THR78
B	LYS79
B	MET80
B	ILE81
B	PHE82
B	HOH302
B	HOH315

site_id	AC6
Number of Residues	23
Details	binding site for Di-peptide HEC B 201 and CYS B 17

Chain	Residue
B	LYS13
B	CYS14
B	ALA15
B	GLN16
B	HIS18
B	LYS27
B	GLU28
B	GLY29
B	PRO30
B	THR40
B	GLY41
B	TYR48
B	THR49
B	ASN52
B	TRP59
B	TYR67
B	THR78
B	LYS79
B	MET80
B	ILE81
B	PHE82
B	HOH302
B	HOH315

site_id	AC7
Number of Residues	23
Details	binding site for Di-peptide HEC C 201 and CYS C 17

Chain	Residue
C	GLY29
C	PRO30
C	THR40
C	GLY41
C	TYR48
C	THR49
C	ASN52
C	TRP59
C	TYR67
C	THR78
C	LYS79
C	MET80
C	ILE81
C	PHE82
C	HOH321
B	ILE81
C	LYS13
C	CYS14
C	ALA15
C	GLN16
C	HIS18
C	LYS27
C	GLU28

site_id	AC8
Number of Residues	22
Details	binding site for Di-peptide HEC C 201 and CYS C 14

Chain	Residue
C	PHE10
C	LYS13
C	ALA15
C	GLN16
C	CYS17
C	HIS18
C	GLU28
C	GLY29
C	PRO30
C	THR40
C	GLY41
C	TYR48
C	THR49
C	ASN52
C	TRP59
C	TYR67
C	THR78
C	LYS79
C	MET80
C	ILE81
C	PHE82
C	HOH321

site_id	AC9
Number of Residues	23
Details	binding site for Di-peptide HEC D 201 and CYS D 17

Chain	Residue
A	ILE81
D	LYS13
D	CYS14
D	ALA15
D	GLN16
D	HIS18
D	LYS27
D	GLU28
D	GLY29
D	PRO30
D	THR40
D	GLY41
D	TYR48
D	THR49
D	ASN52
D	TRP59
D	TYR67
D	THR78
D	LYS79
D	MET80
D	ILE81
D	PHE82
D	HOH314

site_id	AD1
Number of Residues	22
Details	binding site for Di-peptide HEC D 201 and CYS D 14

Chain	Residue
D	PHE10
D	LYS13
D	ALA15
D	GLN16
D	CYS17
D	HIS18
D	GLU28
D	GLY29
D	PRO30
D	THR40
D	GLY41
D	TYR48
D	THR49
D	ASN52
D	TRP59
D	TYR67
D	THR78
D	LYS79
D	MET80
D	ILE81
D	PHE82
D	HOH314

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	8
Details	Binding site: {"description":"covalent"}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	8
Details	Binding site: {"description":"axial binding residue"}

Chain

Residue

Details

site_id	SWS_FT_FI3
Number of Residues	4
Details	Modified residue: {"description":"N-acetylglycine","evidences":[{"source":"PubMed","id":"191069","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI4
Number of Residues	8
Details	Modified residue: {"description":"Phosphotyrosine","evidences":[{"source":"UniProtKB","id":"P62894","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI5
Number of Residues	4
Details	Modified residue: {"description":"N6-succinyllysine","evidences":[{"source":"UniProtKB","id":"P62897","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI6
Number of Residues	4
Details	Modified residue: {"description":"N6-succinyllysine; alternate","evidences":[{"source":"UniProtKB","id":"P62897","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI7
Number of Residues	4
Details	Modified residue: {"description":"N6-acetyllysine","evidences":[{"source":"UniProtKB","id":"P62897","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

		Sequence (fasta)
		PDBx/mmCIF
		PDBML format (no-atom)
		PDB format (full)
		Validation report (PDF)
		EDMap 2fo-fc (MTZ)