2YPT Hydrolase Peptide date Nov 01, 2012
title Crystal Structure Of The Human Nuclear Membrane Zinc Metallo Zmpste24 Mutant (E336a) In Complex With A Synthetic Csim Te From The C-Terminus Of Prelamin A
authors A.C.W.Pike, Y.Y.Dong, A.Quigley, L.Dong, P.Savitsky, C.D.O.Cooper A.Chaikuad, S.Goubin, L.Shrestha, Q.Li, S.Mukhopadhyay, J.Yang, X C.A.Shintre, A.J.Barr, G.Berridge, R.Chalk, J.E.Bray, F.Von Delf A.Bullock, C.Bountra, C.H.Arrowsmith, A.Edwards, N.Burgess-Brow E.P.Carpenter
compound source
Molecule: Caax Prenyl Protease 1 Homolog
Chain: A, B, D, E
Synonym: Farnesylated Proteins-Converting Enzyme 1, Face-1, Protein-Specific Endoprotease 1, Zinc Metalloproteinase Ste Homolog;
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Spodoptera Frugiperda
Expression_system_common: Fall Armyworm
Expression_system_taxid: 7108
Expression_system_cell_line: Sf9
Expression_system_vector_type: Baculovirus
Expression_system_plasmid: Pfb-Ct10hf-Lic

Molecule: Prelamin-Ac
Chain: F, G, H, I
Fragment: C-Terminal Tetrapeptide, Residues 661-664
Synonym: 70 Kda Lamin, Renal Carcinoma Antigen Ny-Ren-32, P
Engineered: Yes

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
symmetry Space Group: P 1
R_factor 0.263 R_Free 0.281
length a length b length c angle alpha angle beta angle gamma
61.320 95.540 132.030 76.26 79.67 72.30
method X-Ray Diffractionresolution 3.80 Å
ligand ZN enzyme Hydrolase E.C. BRENDA
A, D, E, B

Primary referenceThe structural basis of ZMPSTE24-dependent laminopathies., Quigley A, Dong YY, Pike AC, Dong L, Shrestha L, Berridge G, Stansfeld PJ, Sansom MS, Edwards AM, Bountra C, von Delft F, Bullock AN, Burgess-Brown NA, Carpenter EP, Science. 2013 Mar 29;339(6127):1604-7. doi: 10.1126/science.1231513. PMID:23539603
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (557 Kb) [Save to disk]
  • Biological Unit Coordinates (2ypt.pdb1.gz) 143 Kb
  • Biological Unit Coordinates (2ypt.pdb2.gz) 142 Kb
  • Biological Unit Coordinates (2ypt.pdb3.gz) 138 Kb
  • Biological Unit Coordinates (2ypt.pdb4.gz) 137 Kb
  • LPC: Ligand-Protein Contacts for 2YPT
  • CSU: Contacts of Structural Units for 2YPT
  • Structure Factors (989 Kb)
  • Retrieve 2YPT in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2YPT from S2C, [Save to disk]
  • Re-refined 2ypt structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2YPT 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 2YPT
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 2YPT, from MSDmotif at EBI
  • Fold representative 2ypt from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2ypt] [2ypt_E] [2ypt_D] [2ypt_I] [2ypt_A] [2ypt_F] [2ypt_G] [2ypt_H] [2ypt_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 2YPT
  • Community annotation for 2YPT at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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