1NP0 Hydrolase date Jan 16, 2003
title Human Lysosomal Beta-Hexosaminidase Isoform B In Complex Wit Intermediate Analogue Nag-Thiazoline
authors B.L.Mark, D.J.Mahuran, M.M.Cherney, D.Zhao, S.Knapp, M.N.G.James
compound source
Molecule: Beta-Hexosaminidase Subunit Beta
Chain: A, B
Fragment: Propeptide Residues 50-107
Synonym: Beta-N-Acetylhexosaminidase Subunit Beta,Hexosamin Subunit B,Cervical Cancer Proto-Oncogene 7 Protein,Hcc-7,N- Beta-Glucosaminidase Subunit Beta;
 Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Organ: Placenta

Molecule: Beta-Hexosaminidase Subunit Beta Chain B
Chain: C, E
Fragment: Residues 122-311
Synonym: Beta-N-Acetylhexosaminidase Subunit Beta,Hexosamin Subunit B,Cervical Cancer Proto-Oncogene 7 Protein,Hcc-7,N- Beta-Glucosaminidase Subunit Beta;
Ec: 3.2.1.52
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Organ: Placenta

Molecule: Beta-Hexosaminidase Subunit Beta Chain A
Chain: D, F
Fragment: Residues 316-556
Synonym: Beta-N-Acetylhexosaminidase Subunit Beta,Hexosamin Subunit B,Cervical Cancer Proto-Oncogene 7 Protein,Hcc-7,N- Beta-Glucosaminidase Subunit Beta;
Ec: 3.2.1.52
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Organ: Placenta
symmetry Space Group: P 61 2 2
R_factor 0.198 R_Free 0.227
crystal
cell
length a length b length c angle alpha angle beta angle gamma
112.414 112.414 397.232 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.50 Å
ligand GOL, NAG, NGT, SO4 BindingDB enzyme Hydrolase E.C.3.2.1.52 BRENDA
related structures by homologous chain: 1NOU
Gene
Ontology
ChainFunctionProcessComponent
F, D, C, E


Primary referenceCrystal structure of human beta-hexosaminidase B: understanding the molecular basis of Sandhoff and Tay-Sachs disease., Mark BL, Mahuran DJ, Cherney MM, Zhao D, Knapp S, James MN, J Mol Biol 2003 Apr 11;327(5):1093-109. PMID:12662933
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (165 Kb) [Save to disk]
  • Biological Unit Coordinates (1np0.pdb1.gz) 159 Kb
  • Biological Unit Coordinates (1np0.pdb2.gz) 158 Kb
  • Biological Unit Coordinates (1np0.pdb3.gz) 313 Kb
  • LPC: Ligand-Protein Contacts for 1NP0
  • CSU: Contacts of Structural Units for 1NP0
  • Likely Quarternary Molecular Structure file(s) for 1NP0
  • Structure Factors (403 Kb)
  • Retrieve 1NP0 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1NP0 from S2C, [Save to disk]
  • Re-refined 1np0 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 1NP0 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 1NP0
  • 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 1NP0, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1np0a1, region A:200-552 [Jmol] [rasmolscript] [script source]
        - Domain d1np0a2, region A:55-199 [Jmol] [rasmolscript] [script source]
        - Domain d1np0b1, region B:200-552 [Jmol] [rasmolscript] [script source]
        - Domain d1np0b2, region B:55-199 [Jmol] [rasmolscript] [script source]
  • 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: [1np0_C] [1np0] [1np0_E] [1np0_B] [1np0_F] [1np0_D] [1np0_A]
  • SWISS-PROT database: [P07686]
  • Domain organization of [HEXB_HUMAN] by SWISSPFAM
    • Other resources with information on 1NP0
  • Community annotation for 1NP0 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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