5HYB - JenaLib

Title :   CRYSTAL STRUCTURE OF MYRISTOYLATED Y81A MUTANT MMTV MATRIX PROTEIN

Authors :   J. Brynda, J. Dostal, A. Zabransky, M. Dolezal

Date :   01 Feb 16 (Deposition) - 28 Jun 17 (Release) - 28 Jun 17 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.94

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

Keywords :   Myristoylated Protein, Mmtv Mutant, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Brynda, J. Dostal, A. Zabransky, M. Dolezal
Crystal Structure Of Myristoylated Y81A Mutant Mmtv Matrix Protein
To Be Published
PubMed: search

Compounds

Molecule 1 - MATRIX PROTEIN
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector	:	PET-22B
	Expression System Vector Type	:	PLASMID
	Gene	:	GAG
	Mutation	:	YES
	Organism Common	:	MMTV
	Organism Scientific	:	MOUSE MAMMARY TUMOR VIRUS (STRAIN BR6)
	Organism Taxid	:	11758
	Synonym	:	GAG POLYPROTEIN

Structural Features

Chains, Units

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A (1x)	B (1x)
Biological Unit 2 (1x)	:	A (1x)	B (1x)

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (2, 4)

Asymmetric Unit (2, 4)

No.	Name	Count	Type	Full Name
1	MYR	2	Ligand/Ion	MYRISTIC ACID
2	PEG	2	Ligand/Ion	DI(HYDROXYETHYL)ETHER

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	MYR	1	Ligand/Ion	MYRISTIC ACID
2	PEG	1	Ligand/Ion	DI(HYDROXYETHYL)ETHER

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	MYR	1	Ligand/Ion	MYRISTIC ACID
2	PEG	1	Ligand/Ion	DI(HYDROXYETHYL)ETHER

Sites (4, 4)

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:2 , PRO A:47 , GLU A:48 , GLY B:8 , VAL B:15 , LEU B:52 , MYR B:101	binding site for residue MYR A 101
2	AC2	SOFTWARE	MET A:64 , LYS A:65 , ILE A:76 , ALA A:81 , TRP A:84 , HOH A:202	binding site for residue PEG A 102
3	AC3	SOFTWARE	GLY B:61 , MET B:64 , LYS B:65 , ILE B:76 , TRP B:84	binding site for residue PEG B 102
4	AC4	SOFTWARE	GLY A:2 , GLY A:8 , PHE A:12 , LEU A:87 , MYR A:101 , VAL B:3 , SER B:4 , LYS B:7 , PRO B:47 , GLU B:48	binding site for Di-peptide MYR B 101 and GLY B 2

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:91
                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------- Transcript
                  5hyb A  2 GVSGSKGQKLFVSVLQRLLSERGLHVKESSAIEFYQFLIKVSPWFPEEGGLNLQDWKRVGREMKRYAAEHGTDSIPKQAAPIWLQLREILT 92
                                    11        21        31        41        51        61        71        81        91

Chain B from PDB  Type:PROTEIN  Length:91
                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------- Transcript
                  5hyb B  2 GVSGSKGQKLFVSVLQRLLSERGLHVKESSAIEFYQFLIKVSPWFPEEGGLNLQDWKRVGREMKRYAAEHGTDSIPKQAAPIWLQLREILT 92
                                    11        21        31        41        51        61        71        81        91

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 (14, 14)

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
		MYR	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		PEG	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

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

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

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ 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 \| Biol. Unit 2 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
	5hyb
		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
	GAG_MMTVB \| P10258
		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
	GAG_MMTVB \| P10258
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

Description