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(-) Description

Title :  X-RAY CRYSTALLOGRAPHIC STRUCTURE OF AN A-BETA 17_36 BETA-HAIRPIN. X-RAY DIFFRACTOMETER DATA SET. (LVFFAEDCGSNKCAII(SAR)LMV).
 
Authors :  A. G. Kreutzer, R. K. Spencer, J. S. Nowick
Date :  19 Jan 16  (Deposition) - 23 Mar 16  (Release) - 20 Apr 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B,C,D,E,F  (2x)
Biol. Unit 2:  A,B,C  (1x)
Biol. Unit 3:  A,B,C  (2x)
Biol. Unit 4:  D,E,F  (1x)
Biol. Unit 5:  D,E,F  (2x)
Keywords :  Amyloid, Oligomer, Beta-Hairpin, Alzheimer'S, Protein Fibril, De Novo Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. G. Kreutzer, I. L. Hamza, R. K. Spencer, J. S. Nowick
X-Ray Crystallographic Structures Of A Trimer, Dodecamer, And Annular Pore Formed By An A Beta 17-36 Beta-Hairpin.
J. Am. Chem. Soc. V. 138 4634 2016
PubMed-ID: 26967810  |  Reference-DOI: 10.1021/JACS.6B01332

(-) Compounds

Molecule 1 - AMYLOID BETA A4 PROTEIN
    Chains: A, B, C, D, E, F
    Engineered: YES
    Fragment: UNP RESIDUES 687-707
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: ABPP,APPI,APP,ALZHEIMER DISEASE AMYLOID PROTEIN,CEREBRAL VASCULAR AMYLOID PEPTIDE,CVAP,PREA4,PROTEASE NEXIN-II,PN-II
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (2x): ABCDEF
Biological Unit 2 (1x): ABC   
Biological Unit 3 (2x): ABC   
Biological Unit 4 (1x):    DEF
Biological Unit 5 (2x):    DEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 13)

Asymmetric Unit (3, 13)
No.NameCountTypeFull Name
1JEF1Ligand/IonO-(O-(2-AMINOPROPYL)-O'-(2-METHOXYETHYL)POLYPROPYLENEGLYCOL 500)
2ORN6Mod. Amino AcidL-ORNITHINE
3SAR6Mod. Amino AcidSARCOSINE
Biological Unit 1 (3, 26)
No.NameCountTypeFull Name
1JEF2Ligand/IonO-(O-(2-AMINOPROPYL)-O'-(2-METHOXYETHYL)POLYPROPYLENEGLYCOL 500)
2ORN12Mod. Amino AcidL-ORNITHINE
3SAR12Mod. Amino AcidSARCOSINE
Biological Unit 2 (2, 6)
No.NameCountTypeFull Name
1JEF-1Ligand/IonO-(O-(2-AMINOPROPYL)-O'-(2-METHOXYETHYL)POLYPROPYLENEGLYCOL 500)
2ORN3Mod. Amino AcidL-ORNITHINE
3SAR3Mod. Amino AcidSARCOSINE
Biological Unit 3 (2, 12)
No.NameCountTypeFull Name
1JEF-1Ligand/IonO-(O-(2-AMINOPROPYL)-O'-(2-METHOXYETHYL)POLYPROPYLENEGLYCOL 500)
2ORN6Mod. Amino AcidL-ORNITHINE
3SAR6Mod. Amino AcidSARCOSINE
Biological Unit 4 (3, 7)
No.NameCountTypeFull Name
1JEF1Ligand/IonO-(O-(2-AMINOPROPYL)-O'-(2-METHOXYETHYL)POLYPROPYLENEGLYCOL 500)
2ORN3Mod. Amino AcidL-ORNITHINE
3SAR3Mod. Amino AcidSARCOSINE
Biological Unit 5 (3, 14)
No.NameCountTypeFull Name
1JEF2Ligand/IonO-(O-(2-AMINOPROPYL)-O'-(2-METHOXYETHYL)POLYPROPYLENEGLYCOL 500)
2ORN6Mod. Amino AcidL-ORNITHINE
3SAR6Mod. Amino AcidSARCOSINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:4 , PHE D:4binding site for residue JEF D 101

(-) SS Bonds  (6, 6)

Asymmetric Unit
No.Residues
1A:9 -A:14
2B:9 -B:14
3C:9 -C:14
4D:9 -D:14
5E:9 -E:14
6F:9 -F:14

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5HOY)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5HOY)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5HOY)

(-) Exons   (0, 0)

(no "Exon" information available for 5HOY)

(-) 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:21
                                                    
               SCOP domains --------------------- SCOP domains
               CATH domains --------------------- CATH domains
               Pfam domains --------------------- Pfam domains
         Sec.struct. author .eeeeeeee....eeeeeeee Sec.struct. author
                 SAPs(SNPs) --------------------- SAPs(SNPs)
                    PROSITE --------------------- PROSITE
                 Transcript --------------------- Transcript
                  5hoy A  1 kLVFFAEDCGSNKCAIIgLMV 21
                            |       10       |20 
                            |               18-SAR
                            1-ORN                


Chain B from PDB  Type:PROTEIN  Length:21
                                                    
               SCOP domains --------------------- SCOP domains
               CATH domains --------------------- CATH domains
               Pfam domains --------------------- Pfam domains
         Sec.struct. author .eeeeeeee....eeeeeeee Sec.struct. author
                 SAPs(SNPs) --------------------- SAPs(SNPs)
                    PROSITE --------------------- PROSITE
                 Transcript --------------------- Transcript
                  5hoy B  1 kLVFFAEDCGSNKCAIIgLMV 21
                            |       10       |20 
                            |               18-SAR
                            1-ORN                


Chain C from PDB  Type:PROTEIN  Length:21
                                                    
               SCOP domains --------------------- SCOP domains
               CATH domains --------------------- CATH domains
               Pfam domains --------------------- Pfam domains
         Sec.struct. author .eeeeeee......eeeeeee Sec.struct. author
                 SAPs(SNPs) --------------------- SAPs(SNPs)
                    PROSITE --------------------- PROSITE
                 Transcript --------------------- Transcript
                  5hoy C  1 kLVFFAEDCGSNKCAIIgLMV 21
                            |       10       |20 
                            |               18-SAR
                            1-ORN                


Chain D from PDB  Type:PROTEIN  Length:21
                                                    
               SCOP domains --------------------- SCOP domains
               CATH domains --------------------- CATH domains
               Pfam domains --------------------- Pfam domains
         Sec.struct. author .eeeeeee......eeeeeee Sec.struct. author
                 SAPs(SNPs) --------------------- SAPs(SNPs)
                    PROSITE --------------------- PROSITE
                 Transcript --------------------- Transcript
                  5hoy D  1 kLVFFAEDCGSNKCAIIgLMV 21
                            |       10       |20 
                            |               18-SAR
                            1-ORN                


Chain E from PDB  Type:PROTEIN  Length:21
                                                    
               SCOP domains --------------------- SCOP domains
               CATH domains --------------------- CATH domains
               Pfam domains --------------------- Pfam domains
         Sec.struct. author .eeeeeee.......eeeeee Sec.struct. author
                 SAPs(SNPs) --------------------- SAPs(SNPs)
                    PROSITE --------------------- PROSITE
                 Transcript --------------------- Transcript
                  5hoy E  1 kLVFFAEDCGSNKCAIIgLMV 21
                            |       10       |20 
                            |               18-SAR
                            1-ORN                


Chain F from PDB  Type:PROTEIN  Length:21
                                                    
               SCOP domains --------------------- SCOP domains
               CATH domains --------------------- CATH domains
               Pfam domains --------------------- Pfam domains
         Sec.struct. author .eeeeeee......eeeeeee Sec.struct. author
                 SAPs(SNPs) --------------------- SAPs(SNPs)
                    PROSITE --------------------- PROSITE
                 Transcript --------------------- Transcript
                  5hoy F  1 kLVFFAEDCGSNKCAIIgLMV 21
                            |       10       |20 
                            |               18-SAR
                            1-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 5HOY)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5HOY)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5HOY)

(-) Gene Ontology  (111, 111)

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 Related Entries

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        A4_HUMAN | P05067: 1aap 1amb 1amc 1aml 1ba4 1ba6 1bjb 1bjc 1brc 1ca0 1hz3 1iyt 1mwp 1owt 1qcm 1qwp 1qxc 1qyt 1taw 1tkn 1uo7 1uo8 1uoa 1uoi 1x11 1z0q 1ze7 1ze9 1zjd 2beg 2bom 2bp4 2fjz 2fk1 2fk2 2fk3 2fkl 2fma 2g47 2ipu 2lfm 2llm 2lmn 2lmo 2lmp 2lmq 2lnq 2loh 2lp1 2lz3 2lz4 2m4j 2m9r 2m9s 2mgt 2mj1 2mpz 2mvx 2mxu 2nao 2otk 2r0w 2wk3 2y29 2y2a 2y3j 2y3k 2y3l 3ayu 3bae 3bkj 3dxc 3dxd 3dxe 3gci 3ifl 3ifn 3ifo 3ifp 3jq5 3jql 3jti 3ktm 3l33 3l81 3moq 3mxc 3mxy 3nyj 3nyl 3ovj 3ow9 3sv1 3u0t 3umh 3umi 3umk 4hix 4jfn 4m1c 4mdr 4mvi 4mvk 4mvl 4nge 4ojf 4onf 4ong 4pqd 4pwq 4xxd 5aef 5am8 5amb 5buo 5c67 5csz 5how 5hox 5kk3 5kna 5myo

(-) Related Entries Specified in the PDB File

5how 5hox