3MDB Transport Protein Hydrolase Activator date Mar 30, 2010
title Crystal Structure Of The Ternary Complex Of Full Length Cent Alpha-1, Kif13b Fha Domain, And Ip4
authors L.Shen, Y.Tong, W.Tempel, F.Mackenzie, C.H.Arrowsmith, A.M.Edward C.Bountra, J.Weigelt, A.Bochkarev, H.Park, Structural Genomics Consortium (Sgc)
compound source
Molecule: Kinesin-Like Protein Kif13b
Chain: A, B
Fragment: Fha Domain (Unp Residues 440 To 545)
Synonym: Kinesin-Like Protein Gakin
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Kif13b, Gakin, Kiaa0639
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21-Codonplus(De3)-Ril
Expression_system_plasmid: Pet28-Mhl

Molecule: Arf-Gap With Dual Ph Domain-Containing Protein 1
Chain: C, D
Synonym: Centaurin-Alpha-1, Cnt-A1, Putative Mapk-Activatin Pm25;
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Adap1, Centa1
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21-Codonplus(De3)-Ril
Expression_system_plasmid: Pet28-Mhl
symmetry Space Group: P 41 21 2
R_factor 0.225 R_Free 0.277
crystal
cell
length a length b length c angle alpha angle beta angle gamma
115.797 115.797 189.269 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.95 Å
ligand IP9, UNX, ZN enzyme
Gene
Ontology
ChainFunctionProcessComponent
D, C


Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (149 Kb) [Save to disk]
  • Biological Unit Coordinates (3mdb.pdb1.gz) 74 Kb
  • Biological Unit Coordinates (3mdb.pdb2.gz) 71 Kb
  • LPC: Ligand-Protein Contacts for 3MDB
  • CSU: Contacts of Structural Units for 3MDB
  • Structure Factors (423 Kb)
  • Retrieve 3MDB in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3MDB from S2C, [Save to disk]
  • Re-refined 3mdb structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3MDB 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 3MDB
  • 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
  • 3D motif for 3MDB, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3mdb_D] [3mdb_C] [3mdb_A] [3mdb] [3mdb_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 3MDB: [ArfGap] [FHA] [PH ] by SMART
  • Other resources with information on 3MDB
  • Community annotation for 3MDB 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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