1K8R Signaling Protein date Oct 25, 2001
title Crystal Structure Of Ras-Bry2rbd Complex
authors K.Scheffzek, P.Gruenewald, S.Wohlgemuth, W.Kabsch, H.Tu, M.Wigler A.Wittinghofer, C.Herrmann
compound source
Molecule: Transforming Protein P21h-Ras-1
Chain: A
Fragment: Gtp-Bindingcatalytic Domain, Residues 1-166
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Hras Or Hras1
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Ck600k
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pgex-2t

Molecule: Protein Kinase Byr2
Chain: B
Fragment: Ras Binding Domain (Rbd), Residues 71-180
Ec: 2.7.1.-
Engineered: Yes

Organism_scientific: Schizosaccharomyces Pombe
Organism_common: Fission Yeast
Organism_taxid: 4896
Gene: Byr2 Or Ste8 Or Spbc1d7.05
Expression_system: Escherichia Coli Bl21
Expression_system_taxid: 511693
Expression_system_strain: Bl21
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pgex-2t
symmetry Space Group: H 3 2
R_factor 0.235 R_Free 0.305
crystal
cell
length a length b length c angle alpha angle beta angle gamma
139.030 139.030 112.800 90.00 90.00 120.00
method X-Ray Diffractionresolution 3.00 Å
ligand GNP, MG enzyme Transferase E.C.2.7.1 BRENDA
related structures by homologous chain: 1CRR, 1HE8, 1I35
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceThe Ras-Byr2RBD complex: structural basis for Ras effector recognition in yeast., Scheffzek K, Grunewald P, Wohlgemuth S, Kabsch W, Tu H, Wigler M, Wittinghofer A, Herrmann C, Structure (Camb) 2001 Nov;9(11):1043-50. PMID:11709168
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (47 Kb) [Save to disk]
  • Biological Unit Coordinates (1k8r.pdb1.gz) 41 Kb
  • LPC: Ligand-Protein Contacts for 1K8R
  • CSU: Contacts of Structural Units for 1K8R
  • Likely Quarternary Molecular Structure file(s) for 1K8R
  • Structure Factors (204 Kb)
  • Retrieve 1K8R in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1K8R from S2C, [Save to disk]
  • View 1K8R 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 1K8R
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 1K8R, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1k8ra_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1k8rb_, region B [Jmol] [rasmolscript] [script source]
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1k8r_B] [1k8r] [1k8r_A]
  • SWISS-PROT database: [P28829] [P01112]
  • Domain organization of [BYR2_SCHPO] [RASH_HUMAN] by SWISSPFAM
  • Domains found in 1K8R: [RAS] [Ras_bdg_2 ] by SMART
  • Other resources with information on 1K8R
  • Community annotation for 1K8R 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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