1EI8 - JenaLib

Asymmetric Unit (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Title :   STRUCTURAL CONSEQUENCES OF A DISCONTINUITY IN THE REPEATING TRIPEPTIDE SEQUENCE OF A COLLAGEN-LIKE TRIPLE-HELICAL PEPTIDE

Authors :   H. M. Berman, J. Liu

Date :   24 Feb 00 (Deposition) - 09 Sep 03 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

Chains :   Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,C  (1x)
Biol. Unit 2: D,E,F  (1x)
Biol. Unit 3: A,B,C,D,E,F  (1x)

Keywords :   Collagen-Like Peptide, Triple Helix, Contractile Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Bella, J. Liu, R. Kramer, B. Brodsky, H. M. Berman
Conformational Effects Of Gly-X-Gly Interruptions In The Collagen Triple Helix.
J. Mol. Biol. V. 362 298 2006
PubMed-ID: 16919298 | Reference-DOI: 10.1016/J.JMB.2006.07.014
(for further references see the PDB file header)

Molecule 1 - COLLAGEN-LIKE PEPTIDE (PRO-HYP-GLY)4-PG-(PRO-HYP- GLY)5
	Chains	:	A, B, C, D, E, F
	Engineered	:	YES
	Other Details	:	THIS PEPTIDE WAS CHEMICALLY SYNTHESIZED.
	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
Biological Unit 3 (1x)	:	A	B	C	D	E	F

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 53)

No.	Name	Count	Type	Full Name
1	HYP	53	Mod. Amino Acid	4-HYDROXYPROLINE

Biological Unit 1 (1, 26)

No.	Name	Count	Type	Full Name
1	HYP	26	Mod. Amino Acid	4-HYDROXYPROLINE

Biological Unit 2 (1, 27)

No.	Name	Count	Type	Full Name
1	HYP	27	Mod. Amino Acid	4-HYDROXYPROLINE

Biological Unit 3 (1, 53)

No.	Name	Count	Type	Full Name
1	HYP	53	Mod. Amino Acid	4-HYDROXYPROLINE

(no "Site" information available for 1EI8)

(no "SS Bond" information available for 1EI8)

(no "Cis Peptide Bond" information available for 1EI8)

(no "SAP(SNP)/Variant" information available for 1EI8)

(no "PROSITE Motif" information available for 1EI8)

(no "Exon" information available for 1EI8)

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:29
 aligned with Q8T018_DROME | Q8T018 from UniProtKB/TrEMBL  Length:268

    Alignment length:46
                                   150       160       170       180      
         Q8T018_DROME   141 PPGPPGPPGPPGPKGPTKPGPFGPPGPPGPPGPPGPTRPGPYGPPG 186
               SCOP domains d1ei8a_ A:                                     SCOP domains
               CATH domains ---------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------- Pfam domains
         Sec.struct. author .............---------.............--------... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------- PROSITE
                 Transcript ---------------------------------------------- Transcript
                 1ei8 A   1 PpGPpGPpGPpGP---------GPpGPpGPpGPpG--------PpG  29
                             |  |  |10| |      -  | |  |21|  ||    -   || 
                             |  |  |  | |        14 |  |  |  ||       27| 
                             2-HYP |  | |          16-HYP |  ||        28-HYP
                                5-HYP | |             19-HYP ||           
                                   8-HYP|                22-HYP           
                                     11-HYP                 25-HYP        
                                       13                    26

Chain B from PDB  Type:PROTEIN  Length:29
 aligned with Q8T018_DROME | Q8T018 from UniProtKB/TrEMBL  Length:268

    Alignment length:46
                                   150       160       170       180      
         Q8T018_DROME   141 PPGPPGPPGPPGPKGPTKPGPFGPPGPPGPPGPPGPTRPGPYGPPG 186
               SCOP domains d1ei8b_ B:                                     SCOP domains
               CATH domains ---------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------- Pfam domains
         Sec.struct. author .............---------.............--------... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------- PROSITE
                 Transcript ---------------------------------------------- Transcript
                 1ei8 B  31 PpGPpGPpGPpGP---------GPpGPpGPpGPpG--------PpG  59
                             |  |  |40| |      -  | |  |51|  ||    -   || 
                             |  |  |  | |        44 |  |  |  ||       57| 
                            32-HYP |  | |          46-HYP |  ||        58-HYP
                               35-HYP | |             49-HYP ||           
                                  38-HYP|                52-HYP           
                                     41-HYP                 55-HYP        
                                       43                    56

Chain C from PDB  Type:PROTEIN  Length:26
 aligned with Q8T018_DROME | Q8T018 from UniProtKB/TrEMBL  Length:268

    Alignment length:35
                                   150       160       170     
         Q8T018_DROME   141 PPGPPGPPGPPGPKGPTKPGPFGPPGPPGPPGPPG 175
               SCOP domains d1ei8c_ C:                          SCOP domains
               CATH domains ----------------------------------- CATH domains
               Pfam domains ----------------------------------- Pfam domains
         Sec.struct. author .............---------............. Sec.struct. author
                 SAPs(SNPs) ----------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------- PROSITE
                 Transcript ----------------------------------- Transcript
                 1ei8 C  61 PpGPpGPpGPpGP---------GPpGPpGPpGPpG  86
                             |  |  |70| |      -  | |  |81|  | 
                             |  |  |  | |        74 |  |  |  | 
                            62-HYP |  | |          76-HYP |  | 
                               65-HYP | |             79-HYP | 
                                  68-HYP|                82-HYP
                                     71-HYP                 85-HYP
                                       73

Chain D from PDB  Type:PROTEIN  Length:29
 aligned with Q8T018_DROME | Q8T018 from UniProtKB/TrEMBL  Length:268

    Alignment length:46
                                   150       160       170       180      
         Q8T018_DROME   141 PPGPPGPPGPPGPKGPTKPGPFGPPGPPGPPGPPGPTRPGPYGPPG 186
               SCOP domains d1ei8d_ D:                                     SCOP domains
               CATH domains ---------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------- Pfam domains
         Sec.struct. author .............---------.............--------... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------- PROSITE
                 Transcript ---------------------------------------------- Transcript
                 1ei8 D  91 PpGPpGPpGPpGP---------GPpGPpGPpGPpG--------PpG 119
                             |  |  100| |      -  | |  111|  ||    -   || 
                             |  |  |  | |       104 |  |  |  ||      117| 
                            92-HYP |  | |         106-HYP |  ||       118-HYP
                               95-HYP | |            109-HYP ||           
                                  98-HYP|               112-HYP           
                                    101-HYP                115-HYP        
                                      103                   116

Chain E from PDB  Type:PROTEIN  Length:29
 aligned with Q8T018_DROME | Q8T018 from UniProtKB/TrEMBL  Length:268

    Alignment length:46
                                   150       160       170       180      
         Q8T018_DROME   141 PPGPPGPPGPPGPKGPTKPGPFGPPGPPGPPGPPGPTRPGPYGPPG 186
               SCOP domains d1ei8e_ E:                                     SCOP domains
               CATH domains ---------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------- Pfam domains
         Sec.struct. author .............---------.............--------... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------- PROSITE
                 Transcript ---------------------------------------------- Transcript
                 1ei8 E 121 PpGPpGPpGPpGP---------GPpGPpGPpGPpG--------PpG 149
                             |  |  130| |      -  | |  141|  ||    -   || 
                             |  |  |  | |       134 |  |  |  ||      147| 
                           122-HYP |  | |         136-HYP |  ||       148-HYP
                              125-HYP | |            139-HYP ||           
                                 128-HYP|               142-HYP           
                                    131-HYP                145-HYP        
                                      133                   146

Chain F from PDB  Type:PROTEIN  Length:29
 aligned with Q8T018_DROME | Q8T018 from UniProtKB/TrEMBL  Length:268

    Alignment length:46
                                   150       160       170       180      
         Q8T018_DROME   141 PPGPPGPPGPPGPKGPTKPGPFGPPGPPGPPGPPGPTRPGPYGPPG 186
               SCOP domains d1ei8f_ F:                                     SCOP domains
               CATH domains ---------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------- Pfam domains
         Sec.struct. author .............---------.............--------... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------- PROSITE
                 Transcript ---------------------------------------------- Transcript
                 1ei8 F 151 PpGPpGPpGPpGP---------GPpGPpGPpGPpG--------PpG 179
                             |  |  160| |      -  | |  171|  ||    -   || 
                             |  |  |  | |       164 |  |  |  ||      177| 
                           152-HYP |  | |         166-HYP |  ||       178-HYP
                              155-HYP | |            169-HYP ||           
                                 158-HYP|               172-HYP           
                                    161-HYP                175-HYP        
                                      163                   176

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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Designed proteins (167)

Fold: Collagen-like peptides (15)

Superfamily: Collagen-like peptides (15)

Family: Collagen-like peptides (15)

Protein domain: Collagen-like peptides (15)

Synthetic [(pro-hyp-gly)4-pg-(pro-hyp-gly)5] (1)

1a	d1ei8a_	A:
1b	d1ei8b_	B:
1c	d1ei8c_	C:
1d	d1ei8d_	D:
1e	d1ei8e_	E:
1f	d1ei8f_	F:

(no "CATH Domain" information available for 1EI8)

(no "Pfam Domain" information available for 1EI8)

Asymmetric Unit(hide GO term definitions)

(no "Gene Ontology" information available for 1EI8)

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

	Sites
(no "Sites" information available for 1ei8)

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1ei8)

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]
		Biological Unit 3	[ 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 \| Biol. Unit 3 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
	1ei8
		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
	Q8T018_DROME \| Q8T018
		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
	Q8T018_DROME \| Q8T018
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

(no "Entries Sharing at Least One Protein Chain" available for 1EI8)

1qsu	(PRO-HYP-GLY)4-GLU-LYS-GLY(PRO-HYP-GLY)5

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 53)

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 (1, 6)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (0, 0)

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