2X20 - JenaLib

Title :   STRUCTURE OF PERIDININ-CHLOROPHYLL-PROTEIN RECONSTITUTED WITH CHL-B

Authors :   T. Schulte, R. G. Hiller, E. Hofmann

Date :   09 Jan 10 (Deposition) - 09 Feb 10 (Release) - 09 Mar 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.95

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

Keywords :   Light-Harvesting Polypeptide, Light Harvesting Protein, Alpha Helical, Photosynthesis, Chromophore, Chloroplast, Carotenoids (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. Schulte, R. G. Hiller, E. Hofmann
X-Ray Structures Of The Peridinin-Chlorophyll- Protein Reconstituted With Different Chlorophylls.
Febs Lett. V. 584 973 2010
PubMed-ID: 20102711 | Reference-DOI: 10.1016/J.FEBSLET.2010.01.041

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (8, 18)

Asymmetric Unit (8, 18)

No.	Name	Count	Type	Full Name
1	CD	6	Ligand/Ion	CADMIUM ION
2	CHL	1	Ligand/Ion	CHLOROPHYLL B
3	CL	3	Ligand/Ion	CHLORIDE ION
4	DGD	1	Ligand/Ion	DIGALACTOSYL DIACYL GLYCEROL (DGDG)
5	K	1	Ligand/Ion	POTASSIUM ION
6	NA	1	Ligand/Ion	SODIUM ION
7	PEG	1	Ligand/Ion	DI(HYDROXYETHYL)ETHER
8	PID	4	Ligand/Ion	PERIDININ

Biological Unit 1 (4, 14)

No.	Name	Count	Type	Full Name
1	CD	-1	Ligand/Ion	CADMIUM ION
2	CHL	2	Ligand/Ion	CHLOROPHYLL B
3	CL	-1	Ligand/Ion	CHLORIDE ION
4	DGD	2	Ligand/Ion	DIGALACTOSYL DIACYL GLYCEROL (DGDG)
5	K	-1	Ligand/Ion	POTASSIUM ION
6	NA	-1	Ligand/Ion	SODIUM ION
7	PEG	2	Ligand/Ion	DI(HYDROXYETHYL)ETHER
8	PID	8	Ligand/Ion	PERIDININ

Sites (18, 18)

Asymmetric Unit (18, 18)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	PHE M:17 , LEU M:41 , ILE M:48 , ALA M:62 , ALA M:63 , HIS M:66 , LEU M:92 , ALA M:132 , PID M:611 , PID M:612 , PID M:613 , PID M:614 , DGD M:615 , HOH M:2101	BINDING SITE FOR RESIDUE CHL M 601
02	AC2	SOFTWARE	PHE M:17 , TRP M:23 , PHE M:28 , LEU M:29 , LEU M:35 , PRO M:37 , ALA M:40 , PRO M:120 , ALA M:121 , MET M:123 , LYS M:124 , ALA M:132 , TYR M:136 , CHL M:601 , DGD M:615 , HOH M:2048 , HOH M:2068 , HOH M:2183	BINDING SITE FOR RESIDUE PID M 611
03	AC3	SOFTWARE	ILE M:27 , PHE M:28 , GLN M:30 , ALA M:31 , PRO M:32 , ILE M:44 , MET M:47 , VAL M:119 , TYR M:122 , MET M:123 , CHL M:601 , PID M:613 , DGD M:615	BINDING SITE FOR RESIDUE PID M 612
04	AC4	SOFTWARE	MET M:47 , LEU M:59 , VAL M:104 , MET M:105 , VAL M:107 , TYR M:108 , ALA M:121 , LEU M:140 , CHL M:601 , PID M:612 , PID M:614 , DGD M:615 , HOH M:2169 , HOH M:2184 , HOH M:2189	BINDING SITE FOR RESIDUE PID M 613
05	AC5	SOFTWARE	TRP M:23 , LEU M:41 , ALA M:69 , ILE M:70 , VAL M:73 , GLY M:78 , VAL M:79 , THR M:80 , TRP M:85 , ASN M:89 , LEU M:92 , GLU M:101 , PHE M:139 , LYS M:143 , VAL M:146 , GLN M:150 , CHL M:601 , PID M:613 , HOH M:2049 , HOH M:2186 , HOH M:2187	BINDING SITE FOR RESIDUE PID M 614
06	AC6	SOFTWARE	LEU M:29 , PRO M:32 , TYR M:108 , VAL M:111 , SER M:112 , PRO M:120 , ALA M:121 , GLU M:133 , TYR M:136 , GLU M:137 , CHL M:601 , PID M:611 , PID M:612 , PID M:613 , HOH M:2151 , HOH M:2169 , HOH M:2188 , HOH M:2189 , HOH M:2190 , HOH M:2191	BINDING SITE FOR RESIDUE DGD M 615
07	AC7	SOFTWARE	GLU M:2 , ASP M:5 , HOH M:2012 , HOH M:2013 , HOH M:2029 , HOH M:2045	BINDING SITE FOR RESIDUE CD M1151
08	AC8	SOFTWARE	ASP M:5 , ASP M:22 , CL M:1157 , HOH M:2008 , HOH M:2022	BINDING SITE FOR RESIDUE CD M1152
09	AC9	SOFTWARE	ASN M:102 , ASP M:106 , HOH M:2129 , HOH M:2132	BINDING SITE FOR RESIDUE CD M1153
10	BC1	SOFTWARE	MET M:105 , ASP M:109 , ASP M:116 , CL M:1159 , HOH M:2136 , HOH M:2137	BINDING SITE FOR RESIDUE CD M1154
11	BC2	SOFTWARE	GLU M:39 , CL M:1158 , HOH M:2072 , HOH M:2073	BINDING SITE FOR RESIDUE CD M1155
12	BC3	SOFTWARE	GLU M:39 , HOH M:2073 , HOH M:2075	BINDING SITE FOR RESIDUE CD M1156
13	BC4	SOFTWARE	ALA M:0 , ASP M:22 , ASN M:25 , CD M:1152	BINDING SITE FOR RESIDUE CL M1157
14	BC5	SOFTWARE	GLN M:36 , PRO M:37 , LEU M:38 , GLU M:39 , CD M:1155	BINDING SITE FOR RESIDUE CL M1158
15	BC6	SOFTWARE	MET M:105 , ASP M:116 , CD M:1154	BINDING SITE FOR RESIDUE CL M1159
16	BC7	SOFTWARE	GLU M:133 , HOH M:2165 , HOH M:2166	BINDING SITE FOR RESIDUE K M1160
17	BC8	SOFTWARE	ASP M:55 , LYS M:57 , HOH M:2086 , HOH M:2087 , HOH M:2090	BINDING SITE FOR RESIDUE NA M1161
18	BC9	SOFTWARE	ALA M:0 , ASP M:1 , ARG M:94 , LEU M:126 , HOH M:2192 , HOH M:2193 , HOH M:2194 , HOH M:2195 , HOH M:2196	BINDING SITE FOR RESIDUE PEG M1162

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 M from PDB  Type:PROTEIN  Length:151
 aligned with PCP1_AMPCA | P80484 from UniProtKB/Swiss-Prot  Length:370

    Alignment length:151
                                    66        76        86        96       106       116       126       136       146       156       166       176       186       196       206 
           PCP1_AMPCA    57 ADEIGDAAKKLGDASYAFAKEVDWNNGIFLQAPGKLQPLEALKAIDKMIVMGAAADPKLLKAAAEAHHKAIGSVSGPNGVTSRADWDNVNAALGRVIASVPENMVMDVYDSVSKITDPKVPAYMKSLVSGADAEKAYEGFLAFKDVVKKSQ 207
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhh...hhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh....hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2x20 M   0 ADEIGDAAKKLGDASYAFAKEVDWNNGIFLQAPGKLQPLEALKAIDKMIVMGAAADPKLLKAAAEAHHKAIGSVSGPNGVTSRADWDSVNAALGRVIASVPENMVMDVYDSVSKITDPKVPAYMKSLVNGADAEKAYEGFLAFKDVVKKSQ 150
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149

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 (5, 5)

Asymmetric Unit(hide GO term definitions)

Chain M (PCP1_AMPCA | P80484)

molecular function
	GO:0016168	chlorophyll binding	Interacting selectively and non-covalently with chlorophyll; any compound of magnesium complexed in a porphyrin (tetrapyrrole) ring and which functions as a photosynthetic pigment.
biological process
	GO:0018298	protein-chromophore linkage	The covalent or noncovalent attachment of a chromophore to a protein.
cellular component
	GO:0009507	chloroplast	A chlorophyll-containing plastid with thylakoids organized into grana and frets, or stroma thylakoids, and embedded in a stroma.
	GO:0030076	light-harvesting complex	A protein-pigment complex that may be closely or peripherally associated to photosynthetic reaction centers that participate in harvesting and transferring radiant energy to the reaction center.
	GO:0009536	plastid	Any member of a family of organelles found in the cytoplasm of plants and some protists, which are membrane-bounded and contain DNA. Plant plastids develop from a common type, the proplastid.

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
		CD	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		CHL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		CL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		DGD	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		K	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		NA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		PEG	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		PID	[ 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 ]
		AC7	[ RasMol ]	+environment [ RasMol ]
		AC8	[ RasMol ]	+environment [ RasMol ]
		AC9	[ RasMol ]	+environment [ RasMol ]
		BC1	[ RasMol ]	+environment [ RasMol ]
		BC2	[ RasMol ]	+environment [ RasMol ]
		BC3	[ RasMol ]	+environment [ RasMol ]
		BC4	[ RasMol ]	+environment [ RasMol ]
		BC5	[ RasMol ]	+environment [ RasMol ]
		BC6	[ RasMol ]	+environment [ RasMol ]
		BC7	[ RasMol ]	+environment [ RasMol ]
		BC8	[ RasMol ]	+environment [ RasMol ]
		BC9	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2x20)

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

Still Images

Databases and Analysis Tools

Databases

Access by PDB/NDB ID
	2x20
		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
	PCP1_AMPCA \| P80484
		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
	PCP1_AMPCA \| P80484
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

Description