3D9S Membrane Protein date May 27, 2008
title Human Aquaporin 5 (Aqp5) - High Resolution X-Ray Structure
authors R.Horsefield, K.Norden, M.Fellert, A.Backmark, S.Tornroth- Horsefield, A.C.Terwisscha Van Scheltinga, J.Kvassman, P.Kjellbom, U.Johanson, R.Neutze
compound source
Molecule: Aquaporin-5
Chain: A, B, C, D
Synonym: Aqp-5
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Aqp5
Expression_system: Pichia Pastoris
Expression_system_taxid: 4922
Expression_system_strain: X33
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Ppiczb
Other_details: Easyselect Pichia Expression Kit (Invitrogen)
symmetry Space Group: P 21 21 21
length a length b length c angle alpha angle beta angle gamma
90.477 90.644 184.395 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.00 Å
ligand PS6 enzyme
note 3D9S is a representative structure
subcellular loc. Membrane localization by OPM: Eukaryotic plasma membrane
extracellular side
cytoplasmic side
A, D, C, B

Primary referenceHigh-resolution x-ray structure of human aquaporin 5., Horsefield R, Norden K, Fellert M, Backmark A, Tornroth-Horsefield S, Terwisscha van Scheltinga AC, Kvassman J, Kjellbom P, Johanson U, Neutze R, Proc Natl Acad Sci U S A. 2008 Sep 9;105(36):13327-32. Epub 2008 Sep 3. PMID:18768791
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (154 Kb) [Save to disk]
  • Biological Unit Coordinates (3d9s.pdb1.gz) 149 Kb
  • LPC: Ligand-Protein Contacts for 3D9S
  • CSU: Contacts of Structural Units for 3D9S
  • Likely Quarternary Molecular Structure file(s) for 3D9S
  • Structure Factors (720 Kb)
  • Retrieve 3D9S in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3D9S from S2C, [Save to disk]
  • Re-refined 3d9s structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3D9S 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 3D9S
  • 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 3D9S, from MSDmotif at EBI
  • Fold representative 3d9s from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3d9s_B] [3d9s] [3d9s_D] [3d9s_A] [3d9s_C]
  • SWISS-PROT database: [P55064]
  • Belongs to the major intrinsic protein (mip) family according to TCDB.
  • Domain organization of [AQP5_HUMAN] by SWISSPFAM
  • Other resources with information on 3D9S
  • Community annotation for 3D9S 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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