5MKV Hydrolase date Dec 05, 2016
title Crystal Structure Of Human Dihydropyrimidinease-Like 2 (Dpys Collapsin Response Mediator Protein (Crmp2) Residues 13-51
authors R.Sethi, Y.Zheng, T.Krojer, S.Velupillai, C.H.Arrowsmith, A.M.Edw C.Bountra, A.A.Ahmed, F.Von Delft
compound source
Molecule: Dihydropyrimidinase-Related Protein 2
Chain: A, B, C, D
Synonym: Drp-2,Collapsin Response Mediator Protein 2,Crmp-2 33-Like Phosphoprotein 2,Ulip-2;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Dpysl2, Crmp2, Ulip2
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 1 21 1
R_factor 0.167 R_Free 0.200
length a length b length c angle alpha angle beta angle gamma
79.900 157.510 87.420 90.00 93.61 90.00
method X-Ray Diffractionresolution 1.80 Å
ligand EDO enzyme
A, D, C, B

Primary referenceTuning microtubule dynamics to enhance cancer therapy by modulating FER-mediated CRMP2 phosphorylation., Zheng Y, Sethi R, Mangala LS, Taylor C, Goldsmith J, Wang M, Masuda K, Karaminejadranjbar M, Mannion D, Miranda F, Herrero-Gonzalez S, Hellner K, Chen F, Alsaadi A, Albukhari A, Fotso DC, Yau C, Jiang D, Pradeep S, Rodriguez-Aguayo C, Lopez-Berestein G, Knapp S, Gray NS, Campo L, Myers KA, Dhar S, Ferguson D, Bast RC Jr., Sood AK, von Delft F, Ahmed AA, Nat Commun. 2018 Feb 2;9(1):476. doi: 10.1038/s41467-017-02811-7. PMID:29396402
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (321 Kb) [Save to disk]
  • Biological Unit Coordinates (5mkv.pdb1.gz) 314 Kb
  • LPC: Ligand-Protein Contacts for 5MKV
  • CSU: Contacts of Structural Units for 5MKV
  • Structure Factors (5232 Kb)
  • Retrieve 5MKV in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5MKV from S2C, [Save to disk]
  • Re-refined 5mkv structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5MKV 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 5MKV
  • 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
  • Fold representative 5mkv from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5mkv_C] [5mkv_A] [5mkv_D] [5mkv] [5mkv_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5MKV
  • Community annotation for 5MKV at PDBWiki (http://pdbwiki.org)

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