2H5D Hydrolase Hydrolase Inhibitor date May 25, 2006
title 0.9a Resolution Crystal Structure Of Alpha-Lytic Protease Co With A Transition State Analogue, Meosuc-Ala-Ala-Pro-Val Bo
authors C.N.Fuhrmann, D.A.Agard
compound source
Molecule: Alpha-Lytic Protease
Chain: A
Fragment: Mature Protease Domain (Residues 200-397)
Synonym: Alpha-Lytic Endopeptidase
Ec: 3.4.21.12
Other_details: Glycerol Bound To The Catalytic Adduct, Crea Mimic Of The Acylation Transition State Intermediate;
Organism_scientific: Lysobacter Enzymogenes
Organism_taxid: 69
Secretion: Secreted By The Native Bacterium
Other_details: Gene Alpha-Lp

Molecule: Meosuc-Ala-Ala-Pro-Ala Boronic Acid Inhibitor
Chain: B
Engineered: Yes

Synthetic: Yes
symmetry Space Group: P 32 2 1
R_factor
R_Free
crystal
cell
length a length b length c angle alpha angle beta angle gamma
65.768 65.768 79.554 90.00 90.00 120.00
method X-Ray Diffractionresolution 0.90 Å
ligand B2V, GOL, MSU, SO4 enzyme Hydrolase E.C.3.4.21.12 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceSubangstrom crystallography reveals that short ionic hydrogen bonds, and not a His-Asp low-barrier hydrogen bond, stabilize the transition state in serine protease catalysis., Fuhrmann CN, Daugherty MD, Agard DA, J Am Chem Soc. 2006 Jul 19;128(28):9086-102. PMID:16834383
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (122 Kb) [Save to disk]
  • Biological Unit Coordinates (2h5d.pdb1.gz) 116 Kb
  • LPC: Ligand-Protein Contacts for 2H5D
  • CSU: Contacts of Structural Units for 2H5D
  • Likely Quarternary Molecular Structure file(s) for 2H5D
  • Structure Factors (990 Kb)
  • Retrieve 2H5D in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2H5D from S2C, [Save to disk]
  • Re-refined 2h5d structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2H5D 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 2H5D
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 2H5D, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2h5d_B] [2h5d_A] [2h5d]
  • SWISS-PROT database: [P00778]
  • Domain organization of [PRLA_LYSEN] by SWISSPFAM
  • Other resources with information on 2H5D
  • Community annotation for 2H5D 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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