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(-) Description

Title :  NON-HELICAL DNA TRIPLEX FORMS A UNIQUE APTAMER SCAFFOLD FOR HIGH AFFINITY RECOGNITION OF NERVE GROWTH FACTOR
 
Authors :  D. R. Davies, T. E. Edwards
Date :  15 Apr 15  (Deposition) - 10 Jun 15  (Release) - 15 Jul 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.45
Chains :  Asym./Biol. Unit :  A,B,D,E
Keywords :  Complex, Aptamer, Immune System-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. C. Jarvis, D. R. Davies, A. Hisaminato, D. I. Resnicow, S. Gupta, S. M. Waugh, A. Nagabukuro, T. Wadatsu, H. Hishigaki, B. Gawande, C. Zhang, S. K. Wolk, W. S. Mayfield, Y. Nakaishi, A. B. Burgin, L. J. Stewart, T. E. Edwards, A. D. Gelinas, D. J. Schneider, N. Janjic
Non-Helical Dna Triplex Forms A Unique Aptamer Scaffold For High Affinity Recognition Of Nerve Growth Factor.
Structure V. 23 1293 2015
PubMed-ID: 26027732  |  Reference-DOI: 10.1016/J.STR.2015.03.027

(-) Compounds

Molecule 1 - DNA (28-MER)
    Chains: D, E
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES
 
Molecule 2 - BETA-NERVE GROWTH FACTOR
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: NGF, NGFB
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: BETA-NGF

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABDE

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 19)

Asymmetric/Biological Unit (2, 19)
No.NameCountTypeFull Name
1DUZ18Mod. Nucleotide5-(BENZYLCARBAMOYL)-2'-DEOXYURIDINE 5'-(DIHYDROGENPHOSPHATE)
2EPE1Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:75 , DC D:1 , DA D:19 , DG D:20binding site for residue EPE D 101
2AC2SOFTWAREARG A:59 , ARG A:69 , DA D:8 , DC D:9 , DG D:12 , DUZ D:25 , DG D:26 , DUZ D:27 , DG D:28binding site for residues DUZ D 10 and DUZ D 11
3AC3SOFTWARETRP A:21 , TYR A:52 , ILE B:31 , LYS B:32 , PHE B:101 , DUZ D:3 , DG D:4 , DG D:14 , DG D:15 , DUZ D:18 , DA D:19 , DC D:21 , DC D:22binding site for residues DUZ D 16 and DUZ D 17
4AC4SOFTWARETRP A:21 , TYR A:52 , ILE B:31 , LYS B:32 , PHE B:101 , DC D:1 , DA D:2 , DUZ D:3 , DG D:14 , DG D:15 , DUZ D:16 , DA D:19 , DG D:20 , DC D:21 , DC D:22binding site for residues DUZ D 17 and DUZ D 18
5AC5SOFTWARESER A:17 , VAL A:18 , SER A:19 , ARG A:59 , HOH A:201 , DG D:7 , DA D:8 , DUZ D:11 , DG D:12 , DG D:13 , DG D:23 , DG D:26binding site for residues DUZ D 24 and DUZ D 25
6AC6SOFTWAREARG B:59 , ARG B:69 , DA E:8 , DC E:9 , DG E:12 , DUZ E:25 , DG E:26 , DUZ E:27 , DG E:28binding site for residues DUZ E 10 and DUZ E 11
7AC7SOFTWAREPHE A:101 , TRP B:21 , TYR B:52 , DUZ E:3 , DG E:4 , DG E:15 , DUZ E:18 , DA E:19 , DC E:21binding site for residues DUZ E 16 and DUZ E 17
8AC8SOFTWARELYS A:32 , PHE A:101 , HIS B:4 , TRP B:21 , TYR B:52 , DC E:1 , DA E:2 , DUZ E:3 , DG E:15 , DUZ E:16 , DA E:19 , DC E:21binding site for residues DUZ E 17 and DUZ E 18
9AC9SOFTWAREPHE B:7 , SER B:17 , VAL B:18 , SER B:19 , ARG B:59 , DG E:7 , DA E:8 , DUZ E:11 , DG E:12 , DG E:13 , DG E:23 , DG E:26binding site for residues DUZ E 24 and DUZ E 25

(-) SS Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1A:15 -A:80
2A:58 -A:108
3A:68 -A:110
4B:15 -B:80
5B:58 -B:108
6B:68 -B:110

(-) Cis Peptide Bonds  (1, 2)

Asymmetric/Biological Unit
No.Residues
1His B:4 -Pro B:5

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4ZBN)

(-) 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:97
                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee...eeeeee....eee.....eeee..ee....ee..eeeeee.............eeeeeeeeeeeeeeeee..eeeeeeeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------- Transcript
                 4zbn A  11 EFSVCDSVSVWVGDKTTATDIKGKEVMVLGEVNISVFKQYFFETKCRDSGCRGIDSKHWNSYCTTTHTFVKALTMDGKQAAWRFIRIDTACVCVLSR 114
                                    20        30        40   ||   52       |67        77        87        97       107       
                                                            44|           60|                                                
                                                             47            66                                                


Chain B from PDB  Type:PROTEIN  Length:99
                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhh.ee...eeeeee....eee.....eeee..ee...ee..eeeeee.............eeeeeeeeeeeeeeee.eeeeeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------- Transcript
                 4zbn B   4 HPIFHRGEFSVCDSVSVWVGDKTTATDIKGKEVMVLGEVNSVFKQYFFETKCRDSGCRGIDSKHWNSYCTTTHTFVKALTMAAWRFIRIDTACVCVLSR 114
                                    13        23        33        43|       56   ||   71        81        91||     105         
                                                                  43|           60|                        92|                 
                                                                   47            66                         97                 


Chain D from PDB  Type:DNA  Length:28
                                                            
                 4zbn D   1 CAxGAGGACxxGGGGxxxAGCCGxxGxG  28
                              |     10|    |||20   || | 
                              3-DUZ 10-DUZ |||     || | 
                                     11-DUZ|||     || | 
                                          16-DUZ   || | 
                                           17-DUZ  || | 
                                            18-DUZ || | 
                                                  24-DUZ
                                                   25-DUZ
                                                     27-DUZ


Chain E from PDB  Type:DNA  Length:28
                                                            
                 4zbn E   1 CAxGAGGACxxGGGGxxxAGCCGxxGxG  28
                              |     10|    |||20   || | 
                              |     10-DUZ |||     || | 
                              3-DUZ  11-DUZ|||     || | 
                                          16-DUZ   || | 
                                           17-DUZ  || | 
                                            18-DUZ || | 
                                                  24-DUZ
                                                   25-DUZ
                                                     27-DUZ
   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 4ZBN)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4ZBN)

(-) Gene Ontology  (29, 29)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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        NGF_HUMAN | P01138: 1sg1 1www 2ifg 4edw 4edx 5jz7

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