3AI6 - JenaLib

Asymmetric Unit (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   TRIPLE-HELICAL STRUCTURE OF (D-PRO-D-PRO-GLY)9 AT 1.1 A RESOLUTION

Authors :   K. Okuyama, K. Miyama, T. Kawaguchi, N. Nishino

Date :   10 May 10 (Deposition) - 27 Apr 11 (Release) - 27 Apr 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.10

Chains :   Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,C  (1x)
Biol. Unit 2: D,E,F  (1x)

Keywords :   Collagen Helix, D-Enantiomer, Structural Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. Okuyama, K. Miyama, T. Kawaguchi, N. Nishino
Triple-Helical Structure Of (D-Pro-D-Pro-Gly)9
To Be Published
PubMed: search

Molecule 1 - COLLAGEN-LIKE PEPTIDE
	Chains	:	A, B, C, D, E, F
	Engineered	:	YES
	Other Details	:	THIS PEPTIDE ADOPTS A COLLAGEN-HELIX WITH OPPOSITE CHIRALITY.
	Synthetic	:	YES

		1	2	3	4	5	6
Asymmetric Unit	:	A	B	C	D	E	F
Biological Unit 1 (1x)	:	A	B	C
Biological Unit 2 (1x)	:				D	E	F

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 107)

No.	Name	Count	Type	Full Name
1	DPR	107	Mod. Amino Acid	D-PROLINE

Biological Unit 1 (1, 40)

No.	Name	Count	Type	Full Name
1	DPR	40	Mod. Amino Acid	D-PROLINE

Biological Unit 2 (1, 39)

No.	Name	Count	Type	Full Name
1	DPR	39	Mod. Amino Acid	D-PROLINE

(no "Site" information available for 3AI6)

(no "SS Bond" information available for 3AI6)

(no "Cis Peptide Bond" information available for 3AI6)

(no "SAP(SNP)/Variant" information available for 3AI6)

(no "PROSITE Motif" information available for 3AI6)

(no "Exon" information available for 3AI6)

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:27
 aligned with Q80BK4_SHV2 | Q80BK4 from UniProtKB/TrEMBL  Length:99

    Alignment length:27
                                    52        62       
           Q80BK4_SHV2   43 PPGPPGPPGPPGPPGPPGPPGPPGLPG 69
               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
                  3ai6 A  1 xxGxxGxxGxxGxxGxxGxxGxxGxxG 27
                            || || ||10| || || 20 || || 
                            || || || || 14-DPR|| || || 
                            1-DPR || || | 16-DPR || || 
                             2-DPR|| || |  17-DPR|| || 
                               4-DPR || |    19-DPR || 
                                5-DPR|| |     20-DPR|| 
                                  7-DPR |       22-DPR 
                                   8-DPR|        23-DPR
                                    10-DPR         25-DPR
                                     11-DPR         26-DPR

Chain B from PDB  Type:PROTEIN  Length:27
 aligned with Q80BK4_SHV2 | Q80BK4 from UniProtKB/TrEMBL  Length:99

    Alignment length:27
                                    52        62       
           Q80BK4_SHV2   43 PPGPPGPPGPPGPPGPPGPPGPPGLPG 69
               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
                  3ai6 B  1 xxGxxGxxGxxGxxGxxGxxGxxGxxG 27
                            || || ||10| || || 20 || || 
                            || || || || 14-DPR|| || || 
                            1-DPR || || | 16-DPR || || 
                             2-DPR|| || |  17-DPR|| || 
                               4-DPR || |    19-DPR || 
                                5-DPR|| |     20-DPR|| 
                                  7-DPR |       22-DPR 
                                   8-DPR|        23-DPR
                                    10-DPR         25-DPR
                                     11-DPR         26-DPR

Chain C from PDB  Type:PROTEIN  Length:27
 aligned with Q80BK4_SHV2 | Q80BK4 from UniProtKB/TrEMBL  Length:99

    Alignment length:27
                                    52        62       
           Q80BK4_SHV2   43 PPGPPGPPGPPGPPGPPGPPGPPGLPG 69
               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
                  3ai6 C  1 xxGxxGxxGxxGxxGxxGxxGxxGxxG 27
                            || || ||10| || || 20 || || 
                            || || || || 14-DPR|| || || 
                            1-DPR || || | 16-DPR || || 
                             2-DPR|| || |  17-DPR|| || 
                               4-DPR || |    19-DPR || 
                                5-DPR|| |     20-DPR|| 
                                  7-DPR |       22-DPR 
                                   8-DPR|        23-DPR
                                    10-DPR         25-DPR
                                     11-DPR         26-DPR

Chain D from PDB  Type:PROTEIN  Length:27
 aligned with Q80BK4_SHV2 | Q80BK4 from UniProtKB/TrEMBL  Length:99

    Alignment length:27
                                    52        62       
           Q80BK4_SHV2   43 PPGPPGPPGPPGPPGPPGPPGPPGLPG 69
               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
                  3ai6 D  1 xxGxxGxxGxxGxxGxxGxxGxxGxxG 27
                            || || ||10| || || 20 || || 
                            || || || || 14-DPR|| || || 
                            1-DPR || || | 16-DPR || || 
                             2-DPR|| || |  17-DPR|| || 
                               4-DPR || |    19-DPR || 
                                5-DPR|| |     20-DPR|| 
                                  7-DPR |       22-DPR 
                                   8-DPR|        23-DPR
                                    10-DPR         25-DPR
                                     11-DPR         26-DPR

Chain E from PDB  Type:PROTEIN  Length:25
 aligned with Q80BK4_SHV2 | Q80BK4 from UniProtKB/TrEMBL  Length:99

    Alignment length:25
                                    55        65     
           Q80BK4_SHV2   46 PPGPPGPPGPPGPPGPPGPPGLPGL 70
               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
                  3ai6 E  1 xxGxxGxxGxxGxxGxxGxxGxxGx 25
                            || || ||10| || || 20 || |
                            || || || || 14-DPR|| || |
                            1-DPR || || | 16-DPR || |
                             2-DPR|| || |  17-DPR|| |
                               4-DPR || |    19-DPR |
                                5-DPR|| |     20-DPR|
                                  7-DPR |       22-DPR
                                   8-DPR|        23-DPR
                                    10-DPR         25-DPR
                                     11-DPR

Chain F from PDB  Type:PROTEIN  Length:27
 aligned with Q80BK4_SHV2 | Q80BK4 from UniProtKB/TrEMBL  Length:99

    Alignment length:27
                                    52        62       
           Q80BK4_SHV2   43 PPGPPGPPGPPGPPGPPGPPGPPGLPG 69
               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
                  3ai6 F  1 xxGxxGxxGxxGxxGxxGxxGxxGxxG 27
                            || || ||10| || || 20 || || 
                            || || || || 14-DPR|| || || 
                            1-DPR || || | 16-DPR || || 
                             2-DPR|| || |  17-DPR|| || 
                               4-DPR || |    19-DPR || 
                                5-DPR|| |     20-DPR|| 
                                  7-DPR |       22-DPR 
                                   8-DPR|        23-DPR
                                    10-DPR         25-DPR
                                     11-DPR         26-DPR

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 3AI6)

(no "CATH Domain" information available for 3AI6)

(no "Pfam Domain" information available for 3AI6)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D,E,F (Q80BK4_SHV2 | Q80BK4)

cellular component
	GO:0016021		integral component of membrane		The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0016020		membrane		A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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
		DPR	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
(no "Sites" information available for 3ai6)

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3ai6)

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Biol. Unit 1 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)

Access by PDB/NDB ID
	3ai6
		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
	Q80BK4_SHV2 \| Q80BK4
		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
	Q80BK4_SHV2 \| Q80BK4
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/TrEMBL
	Q80BK4_SHV2 \| Q80BK4	:	1k6f 1wzb 1x1k 1ym8 2cuo 2d3f 2d3h 3ah9 3b0s 3b2c

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 107)

Sites (0, 0)

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 (0, 0)

Gene Ontology (2, 2)

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