3NBS - JenaLib

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	LYS A:13 , CYS A:14 , CYS A:17 , HIS A:18 , THR A:28 , GLY A:29 , THR A:40 , GLY A:41 , TYR A:48 , THR A:49 , ASN A:52 , TRP A:59 , TYR A:67 , THR A:78 , HOH A:201 , HOH A:358 , HOH A:403 , PHE B:82 , LEU B:94	BINDING SITE FOR RESIDUE HEM A 105
02	AC2	SOFTWARE	LYS A:55 , ILE A:57 , GLU A:66 , LYS A:73 , TYR A:74 , PRO A:76 , LYS D:55 , GLU D:66 , LYS D:73 , TYR D:74 , PRO D:76	BINDING SITE FOR RESIDUE PG4 A 2002
03	AC3	SOFTWARE	PHE A:82 , LEU A:94 , LYS B:13 , CYS B:14 , CYS B:17 , HIS B:18 , THR B:28 , THR B:40 , GLY B:41 , TYR B:48 , THR B:49 , ASN B:52 , TRP B:59 , TYR B:67 , THR B:78 , HOH B:202 , HOH B:207 , HOH B:320 , PEG B:2004	BINDING SITE FOR RESIDUE HEM B 105
04	AC4	SOFTWARE	GLN A:16 , THR A:28 , GLN B:16 , HEM B:105	BINDING SITE FOR RESIDUE PEG B 2004
05	AC5	SOFTWARE	LYS C:13 , CYS C:14 , CYS C:17 , HIS C:18 , THR C:28 , ARG C:38 , THR C:40 , GLY C:41 , TYR C:48 , THR C:49 , ASN C:52 , TRP C:59 , TYR C:67 , THR C:78 , HOH C:203 , HOH C:362 , HOH C:441 , MET D:80 , PHE D:82 , LEU D:94	BINDING SITE FOR RESIDUE HEM C 105
06	AC6	SOFTWARE	HOH A:420 , TYR B:97 , LYS B:100 , GLU B:104 , TYR C:97 , LYS C:100 , GLU C:104 , LYS D:7 , HOH D:297	BINDING SITE FOR RESIDUE PO4 C 1001
07	AC7	SOFTWARE	LYS B:55 , GLU B:66 , LYS B:73 , TYR B:74 , PRO B:76 , HOH B:389 , LYS C:55 , GLU C:66 , LYS C:73 , TYR C:74 , PRO C:76	BINDING SITE FOR RESIDUE PG4 C 2001
08	AC8	SOFTWARE	PHE C:82 , ILE C:85 , LEU C:94 , LYS D:13 , CYS D:14 , CYS D:17 , HIS D:18 , THR D:28 , THR D:40 , GLY D:41 , TYR D:48 , THR D:49 , ASN D:52 , TRP D:59 , TYR D:67 , THR D:78 , HOH D:204 , HOH D:252 , HOH D:300 , PEG D:2003	BINDING SITE FOR RESIDUE HEM D 105
09	AC9	SOFTWARE	TYR A:97 , LYS A:100 , GLU A:104 , HOH B:345 , LYS C:7 , HOH C:271 , TYR D:97 , LYS D:100 , GLU D:104	BINDING SITE FOR RESIDUE PO4 D 1002
10	BC1	SOFTWARE	THR C:28 , GLN D:16 , HEM D:105	BINDING SITE FOR RESIDUE PEG D 2003

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 4)

Exons (0, 0)

Sequences/Alignments

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:104
 aligned with CYC_HORSE | P00004 from UniProtKB/Swiss-Prot  Length:105

    Alignment length:104
                                    11        21        31        41        51        61        71        81        91       101    
            CYC_HORSE     2 GDVEKGKKIFVQKCAQCHTVEKGGKHKTGPNLHGLFGRKTGQAPGFTYTDANKNKGITWKEETLMEYLENPKKYIPGTKMIFAGIKKKTEREDLIAYLKKATNE 105
               SCOP domains d3nbsa_ A: Mitochondrial cytochrome c                                                                    SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh..................................hhhhhhh....hhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE CYTC  PDB: A:1-102 UniProt: 2-103                                                                     -- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------- Transcript
                 3nbs A   1 GDVEKGKKIFVQKCAQCHTVEKGGKHKTGPNLHGLFGRKTGQAPGFTYTDANKNKGITWKEETLMEYLENPKKYIPGTKMIFAGIKKKTEREDLIAYLKKATNE 104
                                    10        20        30        40        50        60        70        80        90       100

Chain B from PDB  Type:PROTEIN  Length:104
 aligned with CYC_HORSE | P00004 from UniProtKB/Swiss-Prot  Length:105

    Alignment length:104
                                    11        21        31        41        51        61        71        81        91       101    
            CYC_HORSE     2 GDVEKGKKIFVQKCAQCHTVEKGGKHKTGPNLHGLFGRKTGQAPGFTYTDANKNKGITWKEETLMEYLENPKKYIPGTKMIFAGIKKKTEREDLIAYLKKATNE 105
               SCOP domains d3nbsb_ B: Mitochondrial cytochrome c                                                                    SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh..................................hhhhhhh....hhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE CYTC  PDB: B:1-102 UniProt: 2-103                                                                     -- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------- Transcript
                 3nbs B   1 GDVEKGKKIFVQKCAQCHTVEKGGKHKTGPNLHGLFGRKTGQAPGFTYTDANKNKGITWKEETLMEYLENPKKYIPGTKMIFAGIKKKTEREDLIAYLKKATNE 104
                                    10        20        30        40        50        60        70        80        90       100

Chain C from PDB  Type:PROTEIN  Length:104
 aligned with CYC_HORSE | P00004 from UniProtKB/Swiss-Prot  Length:105

    Alignment length:104
                                    11        21        31        41        51        61        71        81        91       101    
            CYC_HORSE     2 GDVEKGKKIFVQKCAQCHTVEKGGKHKTGPNLHGLFGRKTGQAPGFTYTDANKNKGITWKEETLMEYLENPKKYIPGTKMIFAGIKKKTEREDLIAYLKKATNE 105
               SCOP domains d3nbsc_ C: Mitochondrial cytochrome c                                                                    SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh..................................hhhhhh.....hhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE CYTC  PDB: C:1-102 UniProt: 2-103                                                                     -- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------- Transcript
                 3nbs C   1 GDVEKGKKIFVQKCAQCHTVEKGGKHKTGPNLHGLFGRKTGQAPGFTYTDANKNKGITWKEETLMEYLENPKKYIPGTKMIFAGIKKKTEREDLIAYLKKATNE 104
                                    10        20        30        40        50        60        70        80        90       100

Chain D from PDB  Type:PROTEIN  Length:104
 aligned with CYC_HORSE | P00004 from UniProtKB/Swiss-Prot  Length:105

    Alignment length:104
                                    11        21        31        41        51        61        71        81        91       101    
            CYC_HORSE     2 GDVEKGKKIFVQKCAQCHTVEKGGKHKTGPNLHGLFGRKTGQAPGFTYTDANKNKGITWKEETLMEYLENPKKYIPGTKMIFAGIKKKTEREDLIAYLKKATNE 105
               SCOP domains d3nbsd_ D: Mitochondrial cytochrome c                                                                    SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --Cytochrom_C-3nbsD01 D:3-102                                                                         -- Pfam domains (1)
           Pfam domains (2) --Cytochrom_C-3nbsD02 D:3-102                                                                         -- Pfam domains (2)
           Pfam domains (3) --Cytochrom_C-3nbsD03 D:3-102                                                                         -- Pfam domains (3)
           Pfam domains (4) --Cytochrom_C-3nbsD04 D:3-102                                                                         -- Pfam domains (4)
         Sec.struct. author .hhhhhhhhhhhhh..................................hhhhhhh....hhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE CYTC  PDB: D:1-102 UniProt: 2-103                                                                     -- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------- Transcript
                 3nbs D   1 GDVEKGKKIFVQKCAQCHTVEKGGKHKTGPNLHGLFGRKTGQAPGFTYTDANKNKGITWKEETLMEYLENPKKYIPGTKMIFAGIKKKTEREDLIAYLKKATNE 104
                                    10        20        30        40        50        60        70        80        90       100

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Classification and Annotation

SCOP Domains (1, 4)

CATH Domains (0, 0)

Pfam Domains (1, 4)

Gene Ontology (13, 13)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (CYC_HORSE | P00004)

molecular function
	GO:0009055	electron carrier activity	Any molecular entity that serves as an electron acceptor and electron donor in an electron transport chain. An electron transport chain is a process in which a series of electron carriers operate together to transfer electrons from donors to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient.
	GO:0045155	electron transporter, transferring electrons from CoQH2-cytochrome c reductase complex and cytochrome c oxidase complex activity	Enables the directed movement of electrons from the CoQH2-cytochrome c reductase complex and the cytochrome c oxidase complex.
	GO:0020037	heme binding	Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
biological process
	GO:0006915	apoptotic process	A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
	GO:0006123	mitochondrial electron transport, cytochrome c to oxygen	The transfer of electrons from cytochrome c to oxygen that occurs during oxidative phosphorylation, mediated by the multisubunit enzyme known as complex IV.
	GO:0006122	mitochondrial electron transport, ubiquinol to cytochrome c	The transfer of electrons from ubiquinol to cytochrome c that occurs during oxidative phosphorylation, mediated by the multisubunit enzyme known as complex III.
	GO:0055114	oxidation-reduction process	A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
	GO:0043280	positive regulation of cysteine-type endopeptidase activity involved in apoptotic process	Any process that activates or increases the activity of a cysteine-type endopeptidase involved in the apoptotic process.
cellular component
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0005758	mitochondrial intermembrane space	The region between the inner and outer lipid bilayers of the mitochondrial envelope.
	GO:0005739	mitochondrion	A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
	GO:0070469	respiratory chain	The protein complexes that form the electron transport system (the respiratory chain), associated with a cell membrane, usually the plasma membrane (in prokaryotes) or the inner mitochondrial membrane (on eukaryotes). The respiratory chain complexes transfer electrons from an electron donor to an electron acceptor and are associated with a proton pump to create a transmembrane electrochemical gradient.

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	Cis Peptide Bonds
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	3nbs
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 10)

Sites (10, 10)