2OH6 - JenaLib

Biol.Unit 1 - manually (Jmol Viewer)

Asym.Unit - manually (Jmol Viewer)

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Title :   THE CRYSTAL STRUCTURE OF RECOMBINANT CYPOVIRUS POLYHEDRA

Authors :   F. Coulibaly, E. Chiu, K. Ikeda, S. Gutmann, P. W. Haebel, C. Schulze- Briese, H. Mori, P. Metcalf

Date :   09 Jan 07 (Deposition) - 06 Mar 07 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

Chains :   Asym. Unit : A
Biol. Unit 1: A  (12x)

Keywords :   Beta Sandwich, Intracellular Crystal, Nucleotide Binding, Structural Protein, Rna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   F. Coulibaly, E. Chiu, K. Ikeda, S. Gutmann, P. W. Haebel, C. Schulze-Briese, H. Mori, P. Metcalf
The Molecular Organization Of Cypovirus Polyhedra.
Nature V. 446 97 2007
PubMed-ID: 17330045 | Reference-DOI: 10.1038/NATURE05628
(for further references see the PDB file header)

Molecule 1 - POLYHEDRIN
	Chains	:	A
	Engineered	:	YES
	Expression System	:	SPODOPTERA FRUGIPERDA
	Expression System Common	:	FALL ARMYWORM
	Expression System Strain	:	SF21 (IPLB-SF21AE)
	Expression System Taxid	:	7108
	Expression System Vector Type	:	BACULOVIRUS
	Gene	:	POLYHEDRIN
	Mutation	:	YES
	Organism Scientific	:	BOMBYX MORI CYPOVIRUS 1
	Organism Taxid	:	110829
	Strain	:	CPV1
	Synonym	:	C-POLYHEDRIN

		1
Asymmetric Unit	:	A
Biological Unit 1 (12x)	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (6, 7)

No.	Name	Count	Type	Full Name
1	ACE	1	Mod. Amino Acid	ACETYL GROUP
2	ATP	1	Ligand/Ion	ADENOSINE-5'-TRIPHOSPHATE
3	CL	1	Ligand/Ion	CHLORIDE ION
4	CTP	1	Ligand/Ion	CYTIDINE-5'-TRIPHOSPHATE
5	GTP	1	Ligand/Ion	GUANOSINE-5'-TRIPHOSPHATE
6	MG	2	Ligand/Ion	MAGNESIUM ION

Biological Unit 1 (4, 48)

No.	Name	Count	Type	Full Name
1	ACE	12	Mod. Amino Acid	ACETYL GROUP
2	ATP	12	Ligand/Ion	ADENOSINE-5'-TRIPHOSPHATE
3	CL	-1	Ligand/Ion	CHLORIDE ION
4	CTP	12	Ligand/Ion	CYTIDINE-5'-TRIPHOSPHATE
5	GTP	12	Ligand/Ion	GUANOSINE-5'-TRIPHOSPHATE
6	MG	-1	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ALA A:2 , LEU A:31 , HOH A:379	BINDING SITE FOR RESIDUE CL A 249
2	AC2	SOFTWARE	CTP A:254 , HOH A:286	BINDING SITE FOR RESIDUE MG A 250
3	AC3	SOFTWARE	ATP A:253 , HOH A:327	BINDING SITE FOR RESIDUE MG A 251
4	AC4	SOFTWARE	ASN A:9 , ARG A:10 , ARG A:18 , ASP A:156 , HIS A:170 , TYR A:172 , ASN A:173 , LYS A:184 , ATP A:253 , HOH A:326	BINDING SITE FOR RESIDUE GTP A 252
5	AC5	SOFTWARE	LYS A:152 , LYS A:154 , ARG A:155 , ASP A:156 , GLY A:157 , ILE A:159 , LYS A:184 , MG A:251 , GTP A:252 , HOH A:268 , HOH A:269 , HOH A:315 , HOH A:326 , HOH A:327 , HOH A:395	BINDING SITE FOR RESIDUE ATP A 253
6	AC6	SOFTWARE	HIS A:76 , ASN A:77 , ASP A:78 , SER A:79 , TYR A:80 , ASP A:81 , ASP A:96 , ARG A:98 , MG A:250 , HOH A:287 , HOH A:288 , HOH A:367	BINDING SITE FOR RESIDUE CTP A 254

(no "SS Bond" information available for 2OH6)

(no "Cis Peptide Bond" information available for 2OH6)

(no "SAP(SNP)/Variant" information available for 2OH6)

(no "PROSITE Motif" information available for 2OH6)

(no "Exon" information available for 2OH6)

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:248
 aligned with O10693_CPVBM | O10693 from UniProtKB/TrEMBL  Length:248

    Alignment length:248
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240        
         O10693_CPVBM     1 MADVAGTSNRDFRGREQRLFNSEQYNYNNSLNGEVSVWVYAYYSDGSVLVINKNSQYKVGISETFKALKEYRKGQHNDSYDEYEVNQSIYYPNGGDARKFHSNAKPRAIQIIFSPSVNVRTIKMAKGNAVSVPDEYLQRSHPWEATGIKYRKIKRDGEIVGYSHYFELPHEYNSISLAVSGVHKNPSSYNVGSAHNVMDVFQSCDLALRFCNRYWAELELVNHYISPNAYPYLDINNHSYGVALSNRQ 248
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -Cypo_polyhedrin-2oh6A01 A:2-248                                                                                                                                                                                                                         Pfam domains
         Sec.struct. author ..........hhhhhhhhhhhhhhhhhhhh....eeeeeeee.....eeeeeeee..eeeeeehhhhhh........hhhhhhhhhhhhhh................eeeeee....hhhhheeeee........hhhhh.....hhhhheeeee..eeeeeeeeee........eeeeeee.............hhhhhhhhhhhheeeeeee.hhhhhhhhh.......ee.....ee........ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2oh6 A   1 xADVAGTSNRDFRGREQRLFNSEQYNYNSSLNGEVSVWVYAYYSDGSVLVINKNSQYKVGISETFKALKEYRKGQHNDSYDEYEVNQSIYYPNGGDARKFHSNAKPRAIQIIFSPSVNVRTIKMAKGNAVSVPDEYLQRSHPWEATGIKYRKIKRDGEIVGYSHYFELPHEYNSISLAVSGVHKNPSSYNVGSAHNVMDVFQSCDLALRFCNRYWAELELVNHYISPNAYPYLDINNHSYGVALSNRQ 248
                            |       10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240        
                            |                                                                                                                                                                                                                                                       
                            1-ACE

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 '\|'

(no "SCOP Domain" information available for 2OH6)

(no "CATH Domain" information available for 2OH6)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: Cypo_polyhedrin] (3)

Family: Cypo_polyhedrin (3)

Bombyx mori cytoplasmic polyhedrosis virus (BmCPV) (3)

Cypo_polyhedrin-2oh6A01

A:2-248

Asymmetric Unit(hide GO term definitions)

Chain A (O10693_CPVBM | O10693)


GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
GO:0005525	GTP binding	Interacting selectively and non-covalently with GTP, guanosine triphosphate.
GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.

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
		ACE	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		ATP	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		CL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		CTP	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		GTP	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MG	[ 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 2oh6)

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

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)

Access by PDB/NDB ID
	2oh6
		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
	O10693_CPVBM \| O10693
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/TrEMBL

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

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
	O10693_CPVBM \| O10693
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/TrEMBL
	O10693_CPVBM \| O10693	:	2oh5 2oh7

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (6, 7)

Sites (6, 6)

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

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (1, 1)

Gene Ontology (3, 3)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File