1KD8 De Novo Protein date Nov 12, 2001
title X-Ray Structure Of The Coiled Coil Gcn4 Acid Base Heterodimer Acid-D12ia16v Base-D12la16l
authors A.E.Keating, V.N.Malashkevich, B.Tidor, P.S.Kim
compound source
Molecule: Gcn4 Acid Base Heterodimer Acid-D12ia16v
Chain: A, C, F
Synonym: Gabh Aiv
Engineered: Yes
Other_details: Coiled Coil Acid Strand
Synthetic: Yes
Other_details: The Peptide Was Chemically Synthesized.

Molecule: Gcn4 Acid Base Heterodimer Base-D12la16l
Chain: B, D, E
Synonym: Gabh Bll
Engineered: Yes
Other_details: Coiled Coil Base Strand

Synthetic: Yes
Other_details: The Peptide Was Chemically Synthesized.
symmetry Space Group: P 41 21 2
R_factor 0.232 R_Free 0.277
length a length b length c angle alpha angle beta angle gamma
86.044 86.044 78.384 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.90 Å
ligand ACE enzyme
note 1KD8 is a representative structure
related structures by homologous chain: 1RB6
Primary referenceSide-chain repacking calculations for predicting structures and stabilities of heterodimeric coiled coils., Keating AE, Malashkevich VN, Tidor B, Kim PS, Proc Natl Acad Sci U S A 2001 Dec 18;98(26):14825-30. PMID:11752430
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (45 Kb) [Save to disk]
  • Biological Unit Coordinates (1kd8.pdb1.gz) 14 Kb
  • Biological Unit Coordinates (1kd8.pdb2.gz) 14 Kb
  • Biological Unit Coordinates (1kd8.pdb3.gz) 15 Kb
  • LPC: Ligand-Protein Contacts for 1KD8
  • CSU: Contacts of Structural Units for 1KD8
  • Likely Quarternary Molecular Structure file(s) for 1KD8
  • Structure Factors (175 Kb)
  • Retrieve 1KD8 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1KD8 from S2C, [Save to disk]
  • Re-refined 1kd8 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1KD8 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 1KD8
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 1KD8, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1kd8a_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1kd8b_, region B [Jmol] [rasmolscript] [script source]
        - Domain d1kd8c_, region C [Jmol] [rasmolscript] [script source]
        - Domain d1kd8d_, region D [Jmol] [rasmolscript] [script source]
        - Domain d1kd8e_, region E [Jmol] [rasmolscript] [script source]
        - Domain d1kd8f_, region F [Jmol] [rasmolscript] [script source]
  • Fold representative 1kd8 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1kd8_A] [1kd8_D] [1kd8_B] [1kd8_C] [1kd8_F] [1kd8_E] [1kd8]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 1KD8
  • Community annotation for 1KD8 at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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