5KKE - JenaLib

Title :   CRYSTAL STRUCTURE OF A DOMAIN-SWAPPED DIMER OF YEAST ISO-1-CYTOCHROME C WITH CYMAL5

Authors :   B. E. Bowler, F. G. Whitby

Date :   21 Jun 16 (Deposition) - 22 Mar 17 (Release) - 22 Mar 17 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.70

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

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

Reference :   L. J. Mcclelland, H. B. Steele, F. G. Whitby, T. C. Mou, D. Holley, J. B. Ross, S. R. Sprang, B. E. Bowler
Cytochrome C Can Form A Well-Defined Binding Pocket For Hydrocarbons.
J. Am. Chem. Soc. V. 138 16770 2016
PubMed-ID: 27990813 | Reference-DOI: 10.1021/JACS.6B10745

Compounds

Molecule 1 - CYTOCHROME C ISO-1
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	CYC1, YJR048W, J1653
	Mutation	:	YES
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE (STRAIN ATCC 204508 / S288C)
	Organism Taxid	:	559292
	Strain	:	ATCC 204508 / S288C

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 7)

Asymmetric Unit (5, 7)

No.	Name	Count	Type	Full Name
1	CL	1	Ligand/Ion	CHLORIDE ION
2	CM5	1	Ligand/Ion	5-CYCLOHEXYL-1-PENTYL-BETA-D-MALTOSIDE
3	GOL	2	Ligand/Ion	GLYCEROL
4	HEM	1	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
5	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 1 (4, 12)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	CM5	2	Ligand/Ion	5-CYCLOHEXYL-1-PENTYL-BETA-D-MALTOSIDE
3	GOL	4	Ligand/Ion	GLYCEROL
4	HEM	2	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
5	SO4	4	Ligand/Ion	SULFATE ION

Sites (6, 6)

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:13 , CYS A:14 , CYS A:17 , HIS A:18 , VAL A:28 , ILE A:35 , SER A:40 , GLY A:41 , TYR A:48 , THR A:49 , ALA A:51 , TRP A:59 , TYR A:67 , ALA A:81 , PHE A:82 , GLY A:83 , LEU A:94 , CM5 A:204 , HOH A:320 , HOH A:330 , HOH A:331 , HOH A:333 , HOH A:347	binding site for residue HEM A 201
2	AC2	SOFTWARE	SER A:2 , ALA A:3 , LYS A:4 , SER A:47 , TYR A:48 , ASN A:52 , HOH A:308 , HOH A:318 , HOH A:352	binding site for residue SO4 A 202
3	AC3	SOFTWARE	PRO A:76 , GLY A:77 , THR A:78 , LYS A:79 , MET A:80 , LYS A:86 , HOH A:307 , HOH A:317	binding site for residue SO4 A 203
4	AC4	SOFTWARE	TYR A:48 , ASN A:52 , LYS A:55 , GLU A:66 , TYR A:67 , LYS A:73 , TYR A:74 , HEM A:201 , HOH A:302 , HOH A:306 , HOH A:315	binding site for residue CM5 A 204
5	AC5	SOFTWARE	GLY A:23 , GLY A:24 , HIS A:26 , GLY A:45 , HOH A:323 , HOH A:324	binding site for residue GOL A 206
6	AC6	SOFTWARE	PHE A:82	binding site for residue GOL A 207

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

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:108
                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhh...................................hhhhhh....hhhhhhhhhhhhhhhh.hhhhhh....hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------ Transcript
                 5kke A  -5 TEFKAGSAKKGATLFKTRCLQCHTVEKGGPHKVGPNLHGIFGRHSGQAEGYSYTDANIKKNVLWDENNMSEYLTNPAKYIPGTKMAFGGLKKEKDRNDLITYLKKASE 103
                                ||   5        15        25        35        45        55        65        75        85        95        
                               -1|                                                                                                      
                                 1

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 (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (10, 10)

Visualization

Interactive Views

Asymmetric Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		CL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		CM5	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		GOL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		HEM	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		SO4	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]
		AC6	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 5kke)

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

Still Images

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Asym. Unit - sites PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 1 - sites PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Databases and Analysis Tools

Databases

Access by PDB/NDB ID
	5kke
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	CYC1_YEAST \| P00044
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	(no 'Enzyme Classificator' available)
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Analysis Tools

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	CYC1_YEAST \| P00044
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

Description