3M15 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   A ZN-MEDIATED ASYMMETRIC TRIMER OF A CYTOCHROME CB562 VARIANT (D74A-RIDC1)

Authors :   F. A. Tezcan, T. W. Ni

Date :   04 Mar 10 (Deposition) - 12 Jan 11 (Release) - 12 Jan 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.60

Chains :   Asym./Biol. Unit : A,B,C

Keywords :   Asymmetric, Four-Helix Bundle, Homotrimer, Electron Transport, Heme, Metal-Binding, Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. W. Ni, F. A. Tezcan
Structural Characterization Of A Microperoxidase Inside A Metal-Directed Protein Cage.
Angew. Chem. Int. Ed. Engl. V. 49 7014 2010
PubMed-ID: 20721993 | Reference-DOI: 10.1002/ANIE.201001487

Molecule 1 - SOLUBLE CYTOCHROME B562
	Chains	:	A, B, C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	CYBC
	Mutation	:	YES
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	CYTOCHROME B-562

		1	2	3
Asymmetric/Biological Unit	:	A	B	C

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 5)

No.	Name	Count	Type	Full Name
1	HEM	3	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
2	ZN	2	Ligand/Ion	ZINC ION

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU A:4 , MET A:7 , LEU A:10 , LEU A:14 , MET A:33 , PRO A:45 , PRO A:46 , PHE A:61 , GLY A:64 , PHE A:65 , LEU A:68 , CYS A:98 , CYS A:101 , HIS A:102 , ARG A:106 , HOH A:113 , HOH A:115 , HIS C:102 , ARG C:106	BINDING SITE FOR RESIDUE HEM A 150
2	AC2	SOFTWARE	HIS A:73 , HIS A:77 , HIS B:59 , HIS C:59	BINDING SITE FOR RESIDUE ZN A 107
3	AC3	SOFTWARE	GLU B:4 , MET B:7 , LEU B:10 , ASN B:11 , LEU B:14 , MET B:33 , PRO B:45 , PRO B:46 , PHE B:61 , GLY B:64 , PHE B:65 , CYS B:98 , CYS B:101 , HIS B:102 , TYR B:105 , ARG B:106	BINDING SITE FOR RESIDUE HEM B 150
4	AC4	SOFTWARE	HIS A:59 , HIS B:73 , HIS B:77 , HIS C:77	BINDING SITE FOR RESIDUE ZN B 107
5	AC5	SOFTWARE	LYS A:15 , GLU C:4 , MET C:7 , GLU C:8 , ASN C:11 , LEU C:14 , PRO C:45 , PRO C:46 , PHE C:61 , PHE C:65 , LEU C:94 , CYS C:98 , CYS C:101 , HIS C:102 , TYR C:105 , ARG C:106	BINDING SITE FOR RESIDUE HEM C 150

(no "SS Bond" information available for 3M15)

(no "Cis Peptide Bond" information available for 3M15)

(no "SAP(SNP)/Variant" information available for 3M15)

(no "PROSITE Motif" information available for 3M15)

(no "Exon" information available for 3M15)

Asymmetric/Biological 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:106
 aligned with C562_ECOLX | P0ABE7 from UniProtKB/Swiss-Prot  Length:128

    Alignment length:106
                                    32        42        52        62        72        82        92       102       112       122      
           C562_ECOLX    23 ADLEDNMETLNDNLKVIEKADNAAQVKDALTKMRAAALDAQKATPPKLEDKSPDSPEMKDFRHGFDILVGQIDDALKLANEGKVKEAQAAAEQLKTTRNAYHQKYR 128
               SCOP domains d3m15a_ A: automated matches                                                                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh...hhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------- Transcript
                 3m15 A   1 ADLEDNMETLNDNLKVIEKADNAAQVKDALTKMAAAAADAWSATPPKLEDKSPDSPEMHDFRHGFWILIGQIHAALHLANEGKVKEAQAAAEQLKTTCNACHQKYR 106
                                    10        20        30        40        50        60        70        80        90       100

Chain B from PDB  Type:PROTEIN  Length:106
 aligned with C562_ECOLX | P0ABE7 from UniProtKB/Swiss-Prot  Length:128

    Alignment length:106
                                    32        42        52        62        72        82        92       102       112       122      
           C562_ECOLX    23 ADLEDNMETLNDNLKVIEKADNAAQVKDALTKMRAAALDAQKATPPKLEDKSPDSPEMKDFRHGFDILVGQIDDALKLANEGKVKEAQAAAEQLKTTRNAYHQKYR 128
               SCOP domains d3m15b_ B: automated matches                                                                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh...hhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------- Transcript
                 3m15 B   1 ADLEDNMETLNDNLKVIEKADNAAQVKDALTKMAAAAADAWSATPPKLEDKSPDSPEMHDFRHGFWILIGQIHAALHLANEGKVKEAQAAAEQLKTTCNACHQKYR 106
                                    10        20        30        40        50        60        70        80        90       100

Chain C from PDB  Type:PROTEIN  Length:106
 aligned with C562_ECOLX | P0ABE7 from UniProtKB/Swiss-Prot  Length:128

    Alignment length:106
                                    32        42        52        62        72        82        92       102       112       122      
           C562_ECOLX    23 ADLEDNMETLNDNLKVIEKADNAAQVKDALTKMRAAALDAQKATPPKLEDKSPDSPEMKDFRHGFDILVGQIDDALKLANEGKVKEAQAAAEQLKTTRNAYHQKYR 128
               SCOP domains d3m15c_ C: automated matches                                                                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) Cytochrom_B562-3m15C01 C:1-106                                                                             Pfam domains (1)
           Pfam domains (2) Cytochrom_B562-3m15C02 C:1-106                                                                             Pfam domains (2)
           Pfam domains (3) Cytochrom_B562-3m15C03 C:1-106                                                                             Pfam domains (3)
         Sec.struct. author .hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh...hhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------- Transcript
                 3m15 C   1 ADLEDNMETLNDNLKVIEKADNAAQVKDALTKMAAAAADAWSATPPKLEDKSPDSPEMHDFRHGFWILIGQIHAALHLANEGKVKEAQAAAEQLKTTCNACHQKYR 106
                                    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 '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All alpha proteins (14657)

Fold: Four-helical up-and-down bundle (308)

Superfamily: Cytochromes (82)

Family: Cytochrome b562 (38)

Protein domain: automated matches (32)

Escherichia coli [TaxId: 562] (31)

1a	d3m15a_	A:
1b	d3m15b_	B:
1c	d3m15c_	C:

(no "CATH Domain" information available for 3M15)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: Cytochrom_B562] (14)

Family: Cytochrom_B562 (14)

Escherichia coli (13)

1a	Cytochrom_B562-3m15C01	C:1-106
1b	Cytochrom_B562-3m15C02	C:1-106
1c	Cytochrom_B562-3m15C03	C:1-106

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,C (C562_ECOLX | P0ABE7)

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:0020037	heme binding	Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
	GO:0005506	iron ion binding	Interacting selectively and non-covalently with iron (Fe) ions.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
biological process
	GO:0022900	electron transport chain	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: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.
cellular component
	GO:0042597	periplasmic space	The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).

Asymmetric/Biological Unit
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 5)

Sites (5, 5)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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