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(-) Description

Title :  LVFFA SEGMENT FROM ALZHEIMER'S AMYLOID-BETA DISPLAYED ON 42-MEMBERED MACROCYCLE SCAFFOLD, BROMIDE DERIVATIVE
 
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 :  1.99
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, Beta Strand, 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 LV(4BF)FA(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  (6, 44)

Asymmetric Unit (6, 44)
No.NameCountTypeFull Name
14BF8Mod. Amino Acid4-BROMO-L-PHENYLALANINE
2CL7Ligand/IonCHLORIDE ION
3GOL3Ligand/IonGLYCEROL
4HAO8Mod. Amino Acid{[3-(HYDRAZINOCARBONYL)-4-METHOXYPHENYL]AMINO}(OXO)ACETIC ACID
5IPA2Ligand/IonISOPROPYL ALCOHOL
6ORN16Mod. Amino AcidL-ORNITHINE
Biological Unit 1 (4, 19)
No.NameCountTypeFull Name
14BF4Mod. Amino Acid4-BROMO-L-PHENYLALANINE
2CL-1Ligand/IonCHLORIDE ION
3GOL3Ligand/IonGLYCEROL
4HAO4Mod. Amino Acid{[3-(HYDRAZINOCARBONYL)-4-METHOXYPHENYL]AMINO}(OXO)ACETIC ACID
5IPA-1Ligand/IonISOPROPYL ALCOHOL
6ORN8Mod. Amino AcidL-ORNITHINE
Biological Unit 2 (5, 18)
No.NameCountTypeFull Name
14BF4Mod. Amino Acid4-BROMO-L-PHENYLALANINE
2CL-1Ligand/IonCHLORIDE ION
3GOL1Ligand/IonGLYCEROL
4HAO4Mod. Amino Acid{[3-(HYDRAZINOCARBONYL)-4-METHOXYPHENYL]AMINO}(OXO)ACETIC ACID
5IPA1Ligand/IonISOPROPYL ALCOHOL
6ORN8Mod. Amino AcidL-ORNITHINE
Biological Unit 3 (5, 19)
No.NameCountTypeFull Name
14BF4Mod. Amino Acid4-BROMO-L-PHENYLALANINE
2CL-1Ligand/IonCHLORIDE ION
3GOL2Ligand/IonGLYCEROL
4HAO4Mod. Amino Acid{[3-(HYDRAZINOCARBONYL)-4-METHOXYPHENYL]AMINO}(OXO)ACETIC ACID
5IPA1Ligand/IonISOPROPYL ALCOHOL
6ORN8Mod. Amino AcidL-ORNITHINE

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWARECL A:12 , ALA C:5 , ORN C:6 , ORN D:10 , LEU H:8BINDING SITE FOR RESIDUE GOL D 11
02AC2SOFTWAREALA A:5 , ORN A:6 , ORN B:10 , GOL C:11 , LEU E:8BINDING SITE FOR RESIDUE GOL B 11
03AC3SOFTWAREORN A:6 , ORN B:10 , GOL B:11 , 4BF C:3 , ALA C:5 , HAO C:7 , HOH C:37BINDING SITE FOR RESIDUE GOL C 11
04AC4SOFTWARELEU D:8 , ORN D:10 , LYS G:9BINDING SITE FOR RESIDUE CL D 12
05AC5SOFTWAREHAO D:7 , LEU D:8 , LYS G:9BINDING SITE FOR RESIDUE CL D 13
06AC6SOFTWARELYS E:9 , ORN G:6 , ORN H:6BINDING SITE FOR RESIDUE CL E 11
07AC7SOFTWAREORN E:6 , ORN F:6 , LYS H:9BINDING SITE FOR RESIDUE CL E 12
08AC8SOFTWARELEU E:1 , ORN E:10 , HOH E:18 , VAL F:2 , ORN F:10BINDING SITE FOR RESIDUE IPA E 13
09AC9SOFTWARELEU F:8 , ORN G:10 , ORN H:10 , HOH H:16BINDING SITE FOR RESIDUE IPA H 11
10BC1SOFTWAREORN H:10BINDING SITE FOR RESIDUE CL H 12
11BC2SOFTWAREORN A:6 , HAO E:7 , LEU E:8 , ORN H:6BINDING SITE FOR RESIDUE CL A 11
12BC3SOFTWAREORN A:6 , ORN D:10 , GOL D:11BINDING SITE FOR RESIDUE CL A 12

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3Q9I)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3Q9I)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3Q9I)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3Q9I)

(-) Exons   (0, 0)

(no "Exon" information available for 3Q9I)

(-) 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
                  3q9i A  1 LVyFAaxLKa 10
                              |  || 10
                              |  ||  |
                              3-4BF  |
                                 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
                  3q9i B  1 LVyFAaxLKa 10
                              |  || 10
                              |  ||  |
                              3-4BF  |
                                 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
                  3q9i C  1 LVyFAaxLKa 10
                              |  || 10
                              |  ||  |
                              3-4BF  |
                                 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
                  3q9i D  1 LVyFAaxLKa 10
                              |  || 10
                              |  ||  |
                              3-4BF  |
                                 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
                  3q9i E  1 LVyFAaxLKa 10
                              |  || 10
                              |  ||  |
                              3-4BF  |
                                 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
                  3q9i F  1 LVyFAaxLKa 10
                              |  || 10
                              |  ||  |
                              3-4BF  |
                                 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 ..ee...... Sec.struct. author
                 SAPs(SNPs) ---------- SAPs(SNPs)
                    PROSITE ---------- PROSITE
                 Transcript ---------- Transcript
                  3q9i G  1 LVyFAaxLKa 10
                              |  || 10
                              |  ||  |
                              3-4BF  |
                                 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 .ee....... Sec.struct. author
                 SAPs(SNPs) ---------- SAPs(SNPs)
                    PROSITE ---------- PROSITE
                 Transcript ---------- Transcript
                  3q9i H  1 LVyFAaxLKa 10
                              |  || 10
                              |  ||  |
                              3-4BF  |
                                 6-ORN
                                  7-HAO
                                    10-ORN
   Legend:   → Mismatch (orange background)
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  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 '|'

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(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 3Q9I)

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(-) Pfam Domains  (0, 0)

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 Related Entries

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(-) Related Entries Specified in the PDB File

3q9g AMYLOIDOGENIC SEGMENTS ON 42-MEMBERED MACROCYCLE FRAMEWORK
3q9h
3q9j