2D4Q Signaling Protein date Oct 22, 2005
title Crystal Structure Of The Sec-Ph Domain Of The Human Neurofibromatosis Type 1 Protein
authors I.D'Angelo, S.Welti, F.Bonneau, K.Scheffzek
compound source
Molecule: Neurofibromin
Chain: A, B
Fragment: Sec14 Homology Domain
Synonym: Neurofibromatosis-Related Protein Nf-1
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Neurofibromin
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Petm11
symmetry Space Group: P 41 21 2
R_factor 0.240 R_Free 0.280
crystal
cell
length a length b length c angle alpha angle beta angle gamma
113.500 113.500 125.600 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.30 Å
ligand OXN, POP enzyme
subcellular loc. Membrane localization by OPM: Eukaryotic plasma membrane
extracellular side
cytoplasmic side
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceA novel bipartite phospholipid-binding module in the neurofibromatosis type 1 protein., D'angelo I, Welti S, Bonneau F, Scheffzek K, EMBO Rep. 2006 Feb;7(2):174-9. PMID:16397625
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (93 Kb) [Save to disk]
  • Biological Unit Coordinates (2d4q.pdb1.gz) 88 Kb
  • LPC: Ligand-Protein Contacts for 2D4Q
  • CSU: Contacts of Structural Units for 2D4Q
  • Likely Quarternary Molecular Structure file(s) for 2D4Q
  • Structure Factors (285 Kb)
  • Retrieve 2D4Q in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2D4Q from S2C, [Save to disk]
  • Re-refined 2d4q structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2D4Q 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 2D4Q
  • 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 2D4Q, from MSDmotif at EBI
  • Fold representative 2d4q from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2d4q_A] [2d4q] [2d4q_B]
  • SWISS-PROT database: [P21359]
  • Domain organization of [NF1_HUMAN] by SWISSPFAM
  • Domain found in 2D4Q: [SEC14 ] by SMART
  • Other resources with information on 2D4Q
  • Community annotation for 2D4Q 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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