1KEX Protein Binding date Nov 18, 2001
title Crystal Structure Of The B1 Domain Of Human Neuropilin-1
authors C.C.Lee, A.Kreusch, D.Mcmullan, K.Ng, G.Spraggon
compound source
Molecule: Neuropilin-1
Chain: A
Fragment: B1 Domain
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Nrp1
Expression_system: Trichoplusia Ni
Expression_system_common: Cabbage Looper
Expression_system_taxid: 7111
Expression_system_vector_type: Baculovirus
Expression_system_vector: Pfastbacht
symmetry Space Group: P 41 21 2
R_factor 0.189 R_Free 0.266
length a length b length c angle alpha angle beta angle gamma
62.827 62.827 88.375 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.90 Å
Primary referenceCrystal Structure of the Human Neuropilin-1 b1 Domain., Lee CC, Kreusch A, McMullan D, Ng K, Spraggon G, Structure (Camb) 2003 Jan;11(1):99-108. PMID:12517344
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (33 Kb) [Save to disk]
  • Biological Unit Coordinates (1kex.pdb1.gz) 29 Kb
  • CSU: Contacts of Structural Units for 1KEX
  • Likely Quarternary Molecular Structure file(s) for 1KEX
  • Structure Factors (86 Kb)
  • Retrieve 1KEX in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1KEX from S2C, [Save to disk]
  • Re-refined 1kex structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1KEX 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 1KEX
  • 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 1KEX, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1kexa_, region A [Jmol] [rasmolscript] [script source]
  • Fold representative 1kex from FSSP and Dali (Families of Structurally Similar Proteins)
  • 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: [1kex] [1kex_A]
  • SWISS-PROT database: [O14786]
  • Domain organization of [NRP1_HUMAN] by SWISSPFAM
  • Domain found in 1KEX: [FA58C ] by SMART
  • Other resources with information on 1KEX
  • Community annotation for 1KEX 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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