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(-) Description

Title :  CRYSTAL STRUCTURE OF MACROCYCLES CONTAINING ABETA 17-23 (LVFFAED) AND ABETA 30-36 (AII(SAR)L(ORN)V)
 
Authors :  R. K. Spencer, H. Li, J. S. Nowick
Date :  02 Dec 13  (Deposition) - 02 Apr 14  (Release) - 09 Jul 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P
Keywords :  Beta-Sheet, Beta-Hairpin, Amyloid, Amyloid Beta-Sheet Mimic, De Novo Protein-Protein Binding Complex, De Novo Protein, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. K. Spencer, H. Li, J. S. Nowick
X-Ray Crystallographic Structures Of Trimers And Higher-Order Oligomeric Assemblies Of A Peptide Derived Fro A Beta (17-36).
J. Am. Chem. Soc. V. 136 5595 2014
PubMed-ID: 24669800  |  Reference-DOI: 10.1021/JA5017409

(-) Compounds

Molecule 1 - CYCLIC HEXADECAPEPTIDE (ORN)LVFFAED(ORN)AII(SAR)L(ORN)V
    Chains: A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12345678910111213141516
Asymmetric/Biological Unit : ABCDEFGHIJKLMNOP

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 75)

Asymmetric/Biological Unit (4, 75)
No.NameCountTypeFull Name
1CL8Ligand/IonCHLORIDE ION
2NA3Ligand/IonSODIUM ION
3ORN48Mod. Amino AcidL-ORNITHINE
4SAR16Mod. Amino AcidSARCOSINE

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREORN A:15 , HOH A:211BINDING SITE FOR RESIDUE CL A 101
02AC2SOFTWAREGLU A:7 , GLU F:7BINDING SITE FOR RESIDUE NA A 102
03AC3SOFTWAREORN A:1 , GLU B:7 , ORN B:9BINDING SITE FOR RESIDUE NA B 101
04AC4SOFTWAREORN C:1 , HOH C:207BINDING SITE FOR RESIDUE CL C 101
05AC5SOFTWAREALA C:10 , HOH F:103BINDING SITE FOR RESIDUE CL C 102
06AC6SOFTWAREORN D:1 , LEU N:14BINDING SITE FOR RESIDUE CL D 101
07AC7SOFTWAREHOH E:203 , HOH E:205 , HOH E:207 , HOH H:207BINDING SITE FOR RESIDUE CL E 101
08AC8SOFTWAREORN G:1 , LEU P:14BINDING SITE FOR RESIDUE CL G 101
09AC9SOFTWAREORN H:1 , HOH H:206BINDING SITE FOR RESIDUE CL H 101
10BC1SOFTWAREHOH J:205 , HOH J:210BINDING SITE FOR RESIDUE CL J 101
11BC2SOFTWAREGLU M:7 , GLU N:7BINDING SITE FOR RESIDUE NA M 101

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4NTR)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4NTR)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4NTR)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4NTR)

(-) Exons   (0, 0)

(no "Exon" information available for 4NTR)

(-) Sequences/Alignments

Asymmetric/Biological 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 .eeeeee...eeeeee Sec.struct. author
                 SAPs(SNPs) ---------------- SAPs(SNPs)
                    PROSITE ---------------- PROSITE
                 Transcript ---------------- Transcript
                  4ntr A  1 aLVFFAEDaAIIgLaV 16
                            |       10  | | 
                            |       9-ORN | 
                            1-ORN      13-SAR
                                         15-ORN


Chain B from PDB  Type:PROTEIN  Length:16
                                               
               SCOP domains ---------------- SCOP domains
               CATH domains ---------------- CATH domains
               Pfam domains ---------------- Pfam domains
         Sec.struct. author .eeeeee...eeeeee Sec.struct. author
                 SAPs(SNPs) ---------------- SAPs(SNPs)
                    PROSITE ---------------- PROSITE
                 Transcript ---------------- Transcript
                  4ntr B  1 aLVFFAEDaAIIgLaV 16
                            |       10  | | 
                            |       9-ORN | 
                            1-ORN      13-SAR
                                         15-ORN


Chain C from PDB  Type:PROTEIN  Length:16
                                               
               SCOP domains ---------------- SCOP domains
               CATH domains ---------------- CATH domains
               Pfam domains ---------------- Pfam domains
         Sec.struct. author .eeeeee...eeeeee Sec.struct. author
                 SAPs(SNPs) ---------------- SAPs(SNPs)
                    PROSITE ---------------- PROSITE
                 Transcript ---------------- Transcript
                  4ntr C  1 aLVFFAEDaAIIgLaV 16
                            |       10  | | 
                            |       9-ORN | 
                            1-ORN      13-SAR
                                         15-ORN


Chain D from PDB  Type:PROTEIN  Length:16
                                               
               SCOP domains ---------------- SCOP domains
               CATH domains ---------------- CATH domains
               Pfam domains ---------------- Pfam domains
         Sec.struct. author .eeeeee...eeeeee Sec.struct. author
                 SAPs(SNPs) ---------------- SAPs(SNPs)
                    PROSITE ---------------- PROSITE
                 Transcript ---------------- Transcript
                  4ntr D  1 aLVFFAEDaAIIgLaV 16
                            |       10  | | 
                            |       9-ORN | 
                            1-ORN      13-SAR
                                         15-ORN


Chain E from PDB  Type:PROTEIN  Length:16
                                               
               SCOP domains ---------------- SCOP domains
               CATH domains ---------------- CATH domains
               Pfam domains ---------------- Pfam domains
         Sec.struct. author .eeeeee...eeeeee Sec.struct. author
                 SAPs(SNPs) ---------------- SAPs(SNPs)
                    PROSITE ---------------- PROSITE
                 Transcript ---------------- Transcript
                  4ntr E  1 aLVFFAEDaAIIgLaV 16
                            |       10  | | 
                            |       9-ORN | 
                            1-ORN      13-SAR
                                         15-ORN


Chain F from PDB  Type:PROTEIN  Length:16
                                               
               SCOP domains ---------------- SCOP domains
               CATH domains ---------------- CATH domains
               Pfam domains ---------------- Pfam domains
         Sec.struct. author .eeeeee...eeeeee Sec.struct. author
                 SAPs(SNPs) ---------------- SAPs(SNPs)
                    PROSITE ---------------- PROSITE
                 Transcript ---------------- Transcript
                  4ntr F  1 aLVFFAEDaAIIgLaV 16
                            |       10  | | 
                            |       9-ORN | 
                            1-ORN      13-SAR
                                         15-ORN


Chain G from PDB  Type:PROTEIN  Length:16
                                               
               SCOP domains ---------------- SCOP domains
               CATH domains ---------------- CATH domains
               Pfam domains ---------------- Pfam domains
         Sec.struct. author .eeeeee...eeeeee Sec.struct. author
                 SAPs(SNPs) ---------------- SAPs(SNPs)
                    PROSITE ---------------- PROSITE
                 Transcript ---------------- Transcript
                  4ntr G  1 aLVFFAEDaAIIgLaV 16
                            |       10  | | 
                            |       9-ORN | 
                            1-ORN      13-SAR
                                         15-ORN


Chain H from PDB  Type:PROTEIN  Length:16
                                               
               SCOP domains ---------------- SCOP domains
               CATH domains ---------------- CATH domains
               Pfam domains ---------------- Pfam domains
         Sec.struct. author .eeeeee...eeeeee Sec.struct. author
                 SAPs(SNPs) ---------------- SAPs(SNPs)
                    PROSITE ---------------- PROSITE
                 Transcript ---------------- Transcript
                  4ntr H  1 aLVFFAEDaAIIgLaV 16
                            |       10  | | 
                            |       9-ORN | 
                            1-ORN      13-SAR
                                         15-ORN


Chain I from PDB  Type:PROTEIN  Length:16
                                               
               SCOP domains ---------------- SCOP domains
               CATH domains ---------------- CATH domains
               Pfam domains ---------------- Pfam domains
         Sec.struct. author .eeeeee...eeeeee Sec.struct. author
                 SAPs(SNPs) ---------------- SAPs(SNPs)
                    PROSITE ---------------- PROSITE
                 Transcript ---------------- Transcript
                  4ntr I  1 aLVFFAEDaAIIgLaV 16
                            |       10  | | 
                            |       9-ORN | 
                            1-ORN      13-SAR
                                         15-ORN


Chain J from PDB  Type:PROTEIN  Length:16
                                               
               SCOP domains ---------------- SCOP domains
               CATH domains ---------------- CATH domains
               Pfam domains ---------------- Pfam domains
         Sec.struct. author .eeeeee...eeeeee Sec.struct. author
                 SAPs(SNPs) ---------------- SAPs(SNPs)
                    PROSITE ---------------- PROSITE
                 Transcript ---------------- Transcript
                  4ntr J  1 aLVFFAEDaAIIgLaV 16
                            |       10  | | 
                            |       9-ORN | 
                            1-ORN      13-SAR
                                         15-ORN


Chain K from PDB  Type:PROTEIN  Length:16
                                               
               SCOP domains ---------------- SCOP domains
               CATH domains ---------------- CATH domains
               Pfam domains ---------------- Pfam domains
         Sec.struct. author .eeeeee...eeeeee Sec.struct. author
                 SAPs(SNPs) ---------------- SAPs(SNPs)
                    PROSITE ---------------- PROSITE
                 Transcript ---------------- Transcript
                  4ntr K  1 aLVFFAEDaAIIgLaV 16
                            |       10  | | 
                            |       9-ORN | 
                            1-ORN      13-SAR
                                         15-ORN


Chain L from PDB  Type:PROTEIN  Length:16
                                               
               SCOP domains ---------------- SCOP domains
               CATH domains ---------------- CATH domains
               Pfam domains ---------------- Pfam domains
         Sec.struct. author .eeeeee...eeeeee Sec.struct. author
                 SAPs(SNPs) ---------------- SAPs(SNPs)
                    PROSITE ---------------- PROSITE
                 Transcript ---------------- Transcript
                  4ntr L  1 aLVFFAEDaAIIgLaV 16
                            |       10  | | 
                            |       9-ORN | 
                            1-ORN      13-SAR
                                         15-ORN


Chain M from PDB  Type:PROTEIN  Length:16
                                               
               SCOP domains ---------------- SCOP domains
               CATH domains ---------------- CATH domains
               Pfam domains ---------------- Pfam domains
         Sec.struct. author .eeeeee...eeeeee Sec.struct. author
                 SAPs(SNPs) ---------------- SAPs(SNPs)
                    PROSITE ---------------- PROSITE
                 Transcript ---------------- Transcript
                  4ntr M  1 aLVFFAEDaAIIgLaV 16
                            |       10  | | 
                            |       9-ORN | 
                            1-ORN      13-SAR
                                         15-ORN


Chain N from PDB  Type:PROTEIN  Length:16
                                               
               SCOP domains ---------------- SCOP domains
               CATH domains ---------------- CATH domains
               Pfam domains ---------------- Pfam domains
         Sec.struct. author .eeeeee...eeeeee Sec.struct. author
                 SAPs(SNPs) ---------------- SAPs(SNPs)
                    PROSITE ---------------- PROSITE
                 Transcript ---------------- Transcript
                  4ntr N  1 aLVFFAEDaAIIgLaV 16
                            |       10  | | 
                            |       9-ORN | 
                            1-ORN      13-SAR
                                         15-ORN


Chain O from PDB  Type:PROTEIN  Length:16
                                               
               SCOP domains ---------------- SCOP domains
               CATH domains ---------------- CATH domains
               Pfam domains ---------------- Pfam domains
         Sec.struct. author .eeeeee...eeeeee Sec.struct. author
                 SAPs(SNPs) ---------------- SAPs(SNPs)
                    PROSITE ---------------- PROSITE
                 Transcript ---------------- Transcript
                  4ntr O  1 aLVFFAEDaAIIgLaV 16
                            |       10  | | 
                            |       9-ORN | 
                            1-ORN      13-SAR
                                         15-ORN


Chain P from PDB  Type:PROTEIN  Length:16
                                               
               SCOP domains ---------------- SCOP domains
               CATH domains ---------------- CATH domains
               Pfam domains ---------------- Pfam domains
         Sec.struct. author .eeeeee...eeeeee Sec.struct. author
                 SAPs(SNPs) ---------------- SAPs(SNPs)
                    PROSITE ---------------- PROSITE
                 Transcript ---------------- Transcript
                  4ntr P  1 aLVFFAEDaAIIgLaV 16
                            |       10  | | 
                            |       9-ORN | 
                            1-ORN      13-SAR
                                         15-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 4NTR)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4NTR)

(-) Pfam Domains  (0, 0)

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(-) Gene Ontology  (0, 0)

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(-) Related Entries Specified in the PDB File

4ntp 4nw8 4nw9