3HNK - JenaLib

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Biological Unit 3 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE DIMERIC ASSEMBLY OF THE CYT CB562 VARIANT RIDC-1

Authors :   E. N. Salgado, R. A. Lewis, J. Brodin, F. A. Tezcan

Date :   31 May 09 (Deposition) - 09 Feb 10 (Release) - 09 Feb 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

Chains :   Asym. Unit : A,B
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: A  (1x)

Keywords :   Electron Transport, Metal Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   E. N. Salgado, X. I. Ambroggio, J. D. Brodin, R. A. Lewis, B. Kuhlman, F. A. Tezcan
Metal Templated Design Of Protein Interfaces.
Proc. Natl. Acad. Sci. Usa V. 107 1827 2010
PubMed-ID: 20080561 | Reference-DOI: 10.1073/PNAS.0906852107

Molecule 1 - SOLUBLE CYTOCHROME B562
	Chains	:	A, B
	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
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:		B
Biological Unit 3 (1x)	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 2)

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

Biological Unit 1 (1, 2)

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

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	HEM	1	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE

Biological Unit 3 (1, 1)

No.	Name	Count	Type	Full Name
1	HEM	1	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU A:4 , MET A:7 , GLU A:8 , ASN A:11 , MET A:33 , PRO A:45 , PRO A:46 , PHE A:61 , PHE A:65 , CYS A:98 , CYS A:101 , HIS A:102 , TYR A:105 , HOH A:195	BINDING SITE FOR RESIDUE HEM A 150
2	AC2	SOFTWARE	GLU B:4 , MET B:7 , ASN B:11 , MET B:33 , PRO B:45 , PRO B:46 , PHE B:61 , PHE B:65 , CYS B:98 , CYS B:101 , HIS B:102 , TYR B:105 , ARG B:106 , HOH B:147 , HOH B:164	BINDING SITE FOR RESIDUE HEM B 150

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

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

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

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

(no "Exon" information available for 3HNK)

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: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 d3hnka_ A: automated matches                                                                               SCOP domains
               CATH domains 3hnkA00 A:1-106  [code=1.20.120.10, no name defined]                                                       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
                 3hnk A   1 ADLEDNMETLNDNLKVIEKADNAAQVKDALTKMAAAAADAWSATPPKLEDKSPDSPEMHDFRHGFWILIGQIHDALHLANEGKVKEAQAAAEQLKTTCNACHQKYR 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 d3hnkb_ B: automated matches                                                                               SCOP domains
               CATH domains 3hnkB00 B:1-106  [code=1.20.120.10, no name defined]                                                       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
                 3hnk B   1 ADLEDNMETLNDNLKVIEKADNAAQVKDALTKMAAAAADAWSATPPKLEDKSPDSPEMHDFRHGFWILIGQIHDALHLANEGKVKEAQAAAEQLKTTCNACHQKYR 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 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	d3hnka_	A:
1b	d3hnkb_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Up-down Bundle (3216)

Topology: Four Helix Bundle (Hemerythrin (Met), subunit A) (300)

Homologous Superfamily: [code=1.20.120.10, no name defined] (45)

Escherichia coli. Organism_taxid: 562. (13)

1a	3hnkA00	A:1-106
1b	3hnkB00	B:1-106

(no "Pfam Domain" information available for 3HNK)

Asymmetric Unit(hide GO term definitions)

Chain A,B (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).

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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3hnk)

Biological Units
	Complete Structure
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	3hnk
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	C562_ECOLX \| P0ABE7
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2bc5	CRYSTAL STRUCTURE OF E. COLI CYTOCHROME B562 WITH ENGINEERED C-TYPE HEME LINKAGES
2qla	CRYSTAL STRUCTURE OF A 16-HELIX BUNDLE ARCHITECTURE PRODUCED BY THE ZINC-MEDIATED SELF ASSEMBLY OF FOUR CYTOCHROME CB562 MOLECULES
3hni	CRYSTAL STRUCTURE OF THE ZN-INDUCED TETRAMER OF THE ENGINEERED CYT CB562 VARIANT RIDC-1
3hnj	CRYSTAL STRUCTURE OF THE ZN-INDUCED TETRAMER OF THE ENGINEERED CYT CB562 VARIANT RIDC-2
3hnl	CRYSTAL STRUCTURE OF THE CU-INDUCED DIMER OF THE ENGINEERED CYT CB562 VARIANT RIDC-1

Description

Compounds

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Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

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Exons (0, 0)

Sequences/Alignments

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SCOP Domains (1, 2)

CATH Domains (1, 2)

Pfam Domains (0, 0)

Gene Ontology (7, 7)

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