Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
(-)Biological Unit 3
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)
Image Biological Unit 3
Biological Unit 3  (Jmol Viewer)

(-) Description

Title :  LVFFA SEGMENT FROM ALZHEIMER'S AMYLOID-BETA DISPLAYED ON 42-MEMBERED MACROCYCLE SCAFFOLD
 
Authors :  C. Liu, M. R. Sawaya, D. Eisenberg, J. S. Nowick, P. Cheng, J. Zheng
Date :  07 Jan 11  (Deposition) - 08 Jun 11  (Release) - 08 Jun 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.25
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H
Biol. Unit 1:  A,B,C,D  (1x)
Biol. Unit 2:  A,B,E,F  (1x)
Biol. Unit 3:  C,D,G,H  (1x)
Keywords :  Beta Sheet Tetramer, Macrocyclic Peptide, Beta-Sheet Mimetic, Protein Fibril (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Liu, M. R. Sawaya, P. N. Cheng, J. Zheng, J. S. Nowick, D. Eisenberg
Characteristics Of Amyloid-Related Oligomers Revealed By Crystal Structures Of Macrocyclic Beta-Sheet Mimics.
J. Am. Chem. Soc. V. 133 6736 2011
PubMed-ID: 21473620  |  Reference-DOI: 10.1021/JA200222N

(-) Compounds

Molecule 1 - CYCLIC PSEUDO-PEPTIDE LVFFA(ORN)(HAO)LK(ORN)
    Chains: A, B, C, D, E, F, G, H
    Engineered: YES
    Other Details: LVFFA SEGMENT FROM ALZHEIMER'S AMYLOID-BETA DISPLAYED ON 42-MEMBERED MACROCYCLE SCAFFOLD
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : ABCDEFGH
Biological Unit 1 (1x): ABCD    
Biological Unit 2 (1x): AB  EF  
Biological Unit 3 (1x):   CD  GH

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 46)

Asymmetric Unit (5, 46)
No.NameCountTypeFull Name
1BU111Ligand/Ion1,4-BUTANEDIOL
2GOL5Ligand/IonGLYCEROL
3HAO8Mod. Amino Acid{[3-(HYDRAZINOCARBONYL)-4-METHOXYPHENYL]AMINO}(OXO)ACETIC ACID
4ORN16Mod. Amino AcidL-ORNITHINE
5SO46Ligand/IonSULFATE ION
Biological Unit 1 (5, 19)
No.NameCountTypeFull Name
1BU12Ligand/Ion1,4-BUTANEDIOL
2GOL4Ligand/IonGLYCEROL
3HAO4Mod. Amino Acid{[3-(HYDRAZINOCARBONYL)-4-METHOXYPHENYL]AMINO}(OXO)ACETIC ACID
4ORN8Mod. Amino AcidL-ORNITHINE
5SO41Ligand/IonSULFATE ION
Biological Unit 2 (5, 21)
No.NameCountTypeFull Name
1BU14Ligand/Ion1,4-BUTANEDIOL
2GOL2Ligand/IonGLYCEROL
3HAO4Mod. Amino Acid{[3-(HYDRAZINOCARBONYL)-4-METHOXYPHENYL]AMINO}(OXO)ACETIC ACID
4ORN8Mod. Amino AcidL-ORNITHINE
5SO43Ligand/IonSULFATE ION
Biological Unit 3 (5, 25)
No.NameCountTypeFull Name
1BU17Ligand/Ion1,4-BUTANEDIOL
2GOL3Ligand/IonGLYCEROL
3HAO4Mod. Amino Acid{[3-(HYDRAZINOCARBONYL)-4-METHOXYPHENYL]AMINO}(OXO)ACETIC ACID
4ORN8Mod. Amino AcidL-ORNITHINE
5SO43Ligand/IonSULFATE ION

(-) Sites  (22, 22)

Asymmetric Unit (22, 22)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREORN F:10 , BU1 F:13 , ORN H:10BINDING SITE FOR RESIDUE SO4 H 11
02AC2SOFTWAREORN E:10 , HOH E:27 , ORN G:10BINDING SITE FOR RESIDUE SO4 E 11
03AC3SOFTWAREORN C:6 , HOH C:25 , ORN E:6 , HAO H:7 , LEU H:8 , HOH H:24BINDING SITE FOR RESIDUE SO4 E 12
04AC4SOFTWAREORN A:6 , ALA C:5 , ORN C:6 , ORN D:10 , GOL D:11 , HOH H:16BINDING SITE FOR RESIDUE SO4 A 11
05AC5SOFTWARELYS E:9 , ORN G:6 , BU1 G:14 , BU1 H:13BINDING SITE FOR RESIDUE SO4 G 11
06AC6SOFTWAREORN A:6 , HAO E:7 , LEU E:8 , ORN H:6 , HOH H:16BINDING SITE FOR RESIDUE SO4 H 12
07AC7SOFTWAREALA A:5 , ORN A:6 , ORN B:10 , HOH B:14BINDING SITE FOR RESIDUE GOL B 11
08AC8SOFTWARESO4 A:11 , ALA C:5 , ORN C:6 , ORN D:10BINDING SITE FOR RESIDUE GOL D 11
09AC9SOFTWAREORN B:10 , HAO C:7BINDING SITE FOR RESIDUE BU1 B 12
10BC1SOFTWAREORN G:6 , SO4 G:11 , PHE H:4 , ALA H:5 , ORN H:6 , HOH H:23BINDING SITE FOR RESIDUE BU1 H 13
11BC2SOFTWAREVAL G:2 , GOL H:21BINDING SITE FOR RESIDUE BU1 G 12
12BC3SOFTWAREORN F:10 , BU1 F:17 , SO4 H:11BINDING SITE FOR RESIDUE BU1 F 13
13BC4SOFTWARELYS E:9 , PHE G:4 , ORN G:6 , LYS G:9 , ORN G:10 , SO4 G:11BINDING SITE FOR RESIDUE BU1 G 14
14BC5SOFTWAREHAO F:7 , BU1 G:19BINDING SITE FOR RESIDUE BU1 H 15
15BC6SOFTWAREPHE E:4 , ALA E:5 , ORN E:6 , ORN F:6BINDING SITE FOR RESIDUE BU1 E 16
16BC7SOFTWAREPHE F:4 , ORN F:6 , ORN F:10 , BU1 F:13 , LYS H:9BINDING SITE FOR RESIDUE BU1 F 17
17BC8SOFTWAREORN C:6 , HAO C:7BINDING SITE FOR RESIDUE BU1 C 18
18BC9SOFTWAREBU1 H:15BINDING SITE FOR RESIDUE BU1 G 19
19CC1SOFTWAREORN F:6 , LYS H:9BINDING SITE FOR RESIDUE BU1 H 20
20CC2SOFTWAREPHE G:4 , BU1 G:12 , VAL H:2BINDING SITE FOR RESIDUE GOL H 21
21CC3SOFTWARELYS A:9 , LEU C:1 , LYS C:9 , ORN C:10BINDING SITE FOR RESIDUE GOL C 22
22CC4SOFTWARELYS B:9 , LYS C:9 , ORN C:10BINDING SITE FOR RESIDUE GOL B 23

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3Q9H)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3Q9H)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3Q9H)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3Q9H)

(-) Exons   (0, 0)

(no "Exon" information available for 3Q9H)

(-) 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:10
                                         
               SCOP domains ---------- SCOP domains
               CATH domains ---------- CATH domains
               Pfam domains ---------- Pfam domains
         Sec.struct. author .eee...... Sec.struct. author
                 SAPs(SNPs) ---------- SAPs(SNPs)
                    PROSITE ---------- PROSITE
                 Transcript ---------- Transcript
                  3q9h A  1 LVFFAaxLKa 10
                                 || 10
                                 6-ORN
                                  7-HAO
                                    10-ORN


Chain B from PDB  Type:PROTEIN  Length:10
                                         
               SCOP domains ---------- SCOP domains
               CATH domains ---------- CATH domains
               Pfam domains ---------- Pfam domains
         Sec.struct. author .eee...... Sec.struct. author
                 SAPs(SNPs) ---------- SAPs(SNPs)
                    PROSITE ---------- PROSITE
                 Transcript ---------- Transcript
                  3q9h B  1 LVFFAaxLKa 10
                                 || 10
                                 6-ORN
                                  7-HAO
                                    10-ORN


Chain C from PDB  Type:PROTEIN  Length:10
                                         
               SCOP domains ---------- SCOP domains
               CATH domains ---------- CATH domains
               Pfam domains ---------- Pfam domains
         Sec.struct. author .eee...... Sec.struct. author
                 SAPs(SNPs) ---------- SAPs(SNPs)
                    PROSITE ---------- PROSITE
                 Transcript ---------- Transcript
                  3q9h C  1 LVFFAaxLKa 10
                                 || 10
                                 6-ORN
                                  7-HAO
                                    10-ORN


Chain D from PDB  Type:PROTEIN  Length:10
                                         
               SCOP domains ---------- SCOP domains
               CATH domains ---------- CATH domains
               Pfam domains ---------- Pfam domains
         Sec.struct. author .eee...... Sec.struct. author
                 SAPs(SNPs) ---------- SAPs(SNPs)
                    PROSITE ---------- PROSITE
                 Transcript ---------- Transcript
                  3q9h D  1 LVFFAaxLKa 10
                                 || 10
                                 6-ORN
                                  7-HAO
                                    10-ORN


Chain E from PDB  Type:PROTEIN  Length:10
                                         
               SCOP domains ---------- SCOP domains
               CATH domains ---------- CATH domains
               Pfam domains ---------- Pfam domains
         Sec.struct. author .ee....... Sec.struct. author
                 SAPs(SNPs) ---------- SAPs(SNPs)
                    PROSITE ---------- PROSITE
                 Transcript ---------- Transcript
                  3q9h E  1 LVFFAaxLKa 10
                                 || 10
                                 6-ORN
                                  7-HAO
                                    10-ORN


Chain F from PDB  Type:PROTEIN  Length:10
                                         
               SCOP domains ---------- SCOP domains
               CATH domains ---------- CATH domains
               Pfam domains ---------- Pfam domains
         Sec.struct. author ..ee...... Sec.struct. author
                 SAPs(SNPs) ---------- SAPs(SNPs)
                    PROSITE ---------- PROSITE
                 Transcript ---------- Transcript
                  3q9h F  1 LVFFAaxLKa 10
                                 || 10
                                 6-ORN
                                  7-HAO
                                    10-ORN


Chain G from PDB  Type:PROTEIN  Length:10
                                         
               SCOP domains ---------- SCOP domains
               CATH domains ---------- CATH domains
               Pfam domains ---------- Pfam domains
         Sec.struct. author .eee...... Sec.struct. author
                 SAPs(SNPs) ---------- SAPs(SNPs)
                    PROSITE ---------- PROSITE
                 Transcript ---------- Transcript
                  3q9h G  1 LVFFAaxLKa 10
                                 || 10
                                 6-ORN
                                  7-HAO
                                    10-ORN


Chain H from PDB  Type:PROTEIN  Length:10
                                         
               SCOP domains ---------- SCOP domains
               CATH domains ---------- CATH domains
               Pfam domains ---------- Pfam domains
         Sec.struct. author eee....... Sec.struct. author
                 SAPs(SNPs) ---------- SAPs(SNPs)
                    PROSITE ---------- PROSITE
                 Transcript ---------- Transcript
                  3q9h H  1 LVFFAaxLKa 10
                                 || 10
                                 6-ORN
                                  7-HAO
                                    10-ORN
   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)

(no "SCOP Domain" information available for 3Q9H)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3Q9H)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3Q9H)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3Q9H)

 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
    BU1  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    HAO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ORN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ 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 ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    BC1  [ RasMol ]  +environment [ RasMol ]
    BC2  [ RasMol ]  +environment [ RasMol ]
    BC3  [ RasMol ]  +environment [ RasMol ]
    BC4  [ RasMol ]  +environment [ RasMol ]
    BC5  [ RasMol ]  +environment [ RasMol ]
    BC6  [ RasMol ]  +environment [ RasMol ]
    BC7  [ RasMol ]  +environment [ RasMol ]
    BC8  [ RasMol ]  +environment [ RasMol ]
    BC9  [ RasMol ]  +environment [ RasMol ]
    CC1  [ RasMol ]  +environment [ RasMol ]
    CC2  [ RasMol ]  +environment [ RasMol ]
    CC3  [ RasMol ]  +environment [ RasMol ]
    CC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3q9h)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]
    Biological Unit 3  [ 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 | 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)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  3q9h
    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

 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

(no "Entries Sharing at Least One Protein Chain" available for 3Q9H)

(-) Related Entries Specified in the PDB File

3q9g 3q9i 3q9j