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(-) Description

Title :  CRYSTAL STRUCTURE OF MACROCYCLES CONTAINING A 17-23 (LV(PHI)FAED) AND A 30-36 (AII(SAR)L(ORN)V)
 
Authors :  J. S. Nowick, R. K. Spencer, H. Li
Date :  02 Dec 13  (Deposition) - 02 Apr 14  (Release) - 09 Jul 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.99
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, Phe19 Changed To P-Iodo- Phenylalanine, 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)LV(PHI)FAED(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  (5, 87)

Asymmetric/Biological Unit (5, 87)
No.NameCountTypeFull Name
1CL5Ligand/IonCHLORIDE ION
2NA2Ligand/IonSODIUM ION
3ORN48Mod. Amino AcidL-ORNITHINE
4PHI16Mod. Amino AcidIODO-PHENYLALANINE
5SAR16Mod. Amino AcidSARCOSINE

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:7 , HOH A:216 , PHE C:5BINDING SITE FOR RESIDUE NA A 101
2AC2SOFTWAREHOH A:222 , ORN B:1 , HOH B:212 , HOH B:214BINDING SITE FOR RESIDUE CL B 101
3AC3SOFTWAREORN E:1 , HOH E:209BINDING SITE FOR RESIDUE CL E 101
4AC4SOFTWAREASP D:8 , LEU E:2 , ASP E:8 , HOH E:212 , LEU F:2 , ORN L:9BINDING SITE FOR RESIDUE NA E 102
5AC5SOFTWAREHOH G:201 , ORN I:1BINDING SITE FOR RESIDUE CL G 101
6AC6SOFTWAREORN H:1 , HOH H:213BINDING SITE FOR RESIDUE CL H 101
7AC7SOFTWAREHOH I:105 , ORN P:1BINDING SITE FOR RESIDUE CL P 101

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4NTP)

(-) 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
                  4ntp A  1 aLVfFAEDaAIIgLaV 16
                            |  |    10  | | 
                            |  |    |   | | 
                            1-ORN   |   | | 
                               4-PHI|   | | 
                                    9-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
                  4ntp B  1 aLVfFAEDaAIIgLaV 16
                            |  |    10  | | 
                            |  |    |   | | 
                            1-ORN   |   | | 
                               4-PHI|   | | 
                                    9-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
                  4ntp C  1 aLVfFAEDaAIIgLaV 16
                            |  |    10  | | 
                            |  |    |   | | 
                            1-ORN   |   | | 
                               4-PHI|   | | 
                                    9-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
                  4ntp D  1 aLVfFAEDaAIIgLaV 16
                            |  |    10  | | 
                            |  |    |   | | 
                            1-ORN   |   | | 
                               4-PHI|   | | 
                                    9-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
                  4ntp E  1 aLVfFAEDaAIIgLaV 16
                            |  |    10  | | 
                            |  |    |   | | 
                            1-ORN   |   | | 
                               4-PHI|   | | 
                                    9-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
                  4ntp F  1 aLVfFAEDaAIIgLaV 16
                            |  |    10  | | 
                            |  |    |   | | 
                            1-ORN   |   | | 
                               4-PHI|   | | 
                                    9-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
                  4ntp G  1 aLVfFAEDaAIIgLaV 16
                            |  |    10  | | 
                            |  |    |   | | 
                            1-ORN   |   | | 
                               4-PHI|   | | 
                                    9-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
                  4ntp H  1 aLVfFAEDaAIIgLaV 16
                            |  |    10  | | 
                            |  |    |   | | 
                            1-ORN   |   | | 
                               4-PHI|   | | 
                                    9-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
                  4ntp I  1 aLVfFAEDaAIIgLaV 16
                            |  |    10  | | 
                            |  |    |   | | 
                            1-ORN   |   | | 
                               4-PHI|   | | 
                                    9-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
                  4ntp J  1 aLVfFAEDaAIIgLaV 16
                            |  |    10  | | 
                            |  |    |   | | 
                            1-ORN   |   | | 
                               4-PHI|   | | 
                                    9-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
                  4ntp K  1 aLVfFAEDaAIIgLaV 16
                            |  |    10  | | 
                            |  |    |   | | 
                            1-ORN   |   | | 
                               4-PHI|   | | 
                                    9-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
                  4ntp L  1 aLVfFAEDaAIIgLaV 16
                            |  |    10  | | 
                            |  |    |   | | 
                            1-ORN   |   | | 
                               4-PHI|   | | 
                                    9-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
                  4ntp M  1 aLVfFAEDaAIIgLaV 16
                            |  |    10  | | 
                            |  |    |   | | 
                            1-ORN   |   | | 
                               4-PHI|   | | 
                                    9-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
                  4ntp N  1 aLVfFAEDaAIIgLaV 16
                            |  |    10  | | 
                            |  |    |   | | 
                            1-ORN   |   | | 
                               4-PHI|   | | 
                                    9-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
                  4ntp O  1 aLVfFAEDaAIIgLaV 16
                            |  |    10  | | 
                            |  |    |   | | 
                            1-ORN   |   | | 
                               4-PHI|   | | 
                                    9-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
                  4ntp P  1 aLVfFAEDaAIIgLaV 16
                            |  |    10  | | 
                            |  |    |   | | 
                            1-ORN   |   | | 
                               4-PHI|   | | 
                                    9-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 4NTP)

(-) CATH Domains  (0, 0)

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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

4ntr 4nw8 4nw9