6D02 De Novo Protein date Apr 10, 2018
title Cross-Alpha Amyloid-Like Structure Alphaaml, 2nd Form
authors S.Q.Zhang, L.Liu, W.F.Degrado
compound source
Molecule: Alpha-Amyloid Peptide Alphaaml
Chain: A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R V, W, X, Y, Z, A, B, C, D, E, F;
Engineered: Yes
 Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: P 21 21 2
R_factor 0.232 R_Free 0.277
crystal
cell
length a length b length c angle alpha angle beta angle gamma
107.546 107.777 99.374 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.50 Å
ligand CO3, MPD, NH2, PO4 enzyme
Primary referenceDesigned peptides that assemble into cross-alpha amyloid-like structures., Zhang SQ, Huang H, Yang J, Kratochvil HT, Lolicato M, Liu Y, Shu X, Liu L, DeGrado WF, Nat Chem Biol. 2018 Jul 30. pii: 10.1038/s41589-018-0105-5. doi:, 10.1038/s41589-018-0105-5. PMID:30061717
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (257 Kb) [Save to disk]
  • Biological Unit Coordinates (6d02.pdb1.gz) 247 Kb
  • LPC: Ligand-Protein Contacts for 6D02
  • CSU: Contacts of Structural Units for 6D02
  • Structure Factors (577 Kb)
  • Retrieve 6D02 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6D02 from S2C, [Save to disk]
    • View 6D02 in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
    • Visual 3D analysis of 6D02
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6d02_R] [6d02_W] [6d02_S] [6d02_M] [6d02_I] [6d02_G] [6d02_N] [6d02_c] [6d02_X] [6d02_e] [6d02_B] [6d02_f] [6d02_L] [6d02_O] [6d02_C] [6d02_T] [6d02_J] [6d02_V] [6d02_E] [6d02_A] [6d02_Q] [6d02_b] [6d02_d] [6d02_K] [6d02_H] [6d02_P] [6d02_Z] [6d02_a] [6d02_F] [6d02_D] [6d02_U] [6d02_Y]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 6D02
  • Community annotation for 6D02 at PDBWiki (http://pdbwiki.org)

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