4IVH - JenaLib

Title :   CRYSTAL STRUCTURE OF QKLVFFAED NONAPEPTIDE SEGMENT FROM AMYLOID BETA INCORPORATED INTO A MACROCYCLIC BETA-SHEET TEMPLATE

Authors :   J. D. Pham, N. Chim, C. W. Goulding, J. S. Nowick

Date :   22 Jan 13 (Deposition) - 31 Jul 13 (Release) - 31 Jul 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.77

Chains :   Asym. Unit : A
Biol. Unit 1: A  (4x)

Keywords :   Amyloid Oligomer, De Novo Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. D. Pham, N. Chim, C. W. Goulding, J. S. Nowick
Structures Of Beta-Amyloid Peptide Oligomers
J. Am. Chem. Soc. 2013
PubMed: search

Compounds

Molecule 1 - CYCLO[GLN-LYS-LEU-VAL-PHE-PHE-ALA-GLU-ASP-(DELTA-LINKED- ORN)-HAO-LYS-HAO-(P-BROMOPHE)-THR-(DELTA-LINKED-ORN)]
	Chains	:	A
	Engineered	:	YES
	Organism Common	:	SYNTHETIC
	Organism Scientific	:	SYNTHETIC CONSTRUCT
	Organism Taxid	:	32630
	Synthetic	:	YES

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 7)

Asymmetric Unit (5, 7)

No.	Name	Count	Type	Full Name
1	4BF	1	Mod. Amino Acid	4-BROMO-L-PHENYLALANINE
2	HAO	2	Mod. Amino Acid	{[3-(HYDRAZINOCARBONYL)-4-METHOXYPHENYL]AMINO}(OXO)ACETIC ACID
3	NA	1	Ligand/Ion	SODIUM ION
4	ORN	2	Mod. Amino Acid	L-ORNITHINE
5	TBU	1	Ligand/Ion	TERTIARY-BUTYL ALCOHOL

Biological Unit 1 (4, 24)

No.	Name	Count	Type	Full Name
1	4BF	4	Mod. Amino Acid	4-BROMO-L-PHENYLALANINE
2	HAO	8	Mod. Amino Acid	{[3-(HYDRAZINOCARBONYL)-4-METHOXYPHENYL]AMINO}(OXO)ACETIC ACID
3	NA	-1	Ligand/Ion	SODIUM ION
4	ORN	8	Mod. Amino Acid	L-ORNITHINE
5	TBU	4	Ligand/Ion	TERTIARY-BUTYL ALCOHOL

Sites (2, 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:16
                                               
               SCOP domains ---------------- SCOP domains
               CATH domains ---------------- CATH domains
               Pfam domains ---------------- Pfam domains
         Sec.struct. author ................ Sec.struct. author
                 SAPs(SNPs) ---------------- SAPs(SNPs)
                    PROSITE ---------------- PROSITE
                 Transcript ---------------- Transcript
                  4ivh A  1 TaQKLVFFAEDaxKxy 16
                             |      10 || ||
                             |        12-ORN
                             2-ORN     13-HAO
                                         15-HAO
                                          16-4BF

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 (0, 0)

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
		4BF	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		HAO	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		NA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		ORN	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		TBU	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

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

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4ivh)

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
	4ivh
		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
	(no 'UniProt ID/Accession number' available) \|
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProt

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
	(no 'UniProt ID/Accession number' available) \|
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT

Description