1jwr: Difference between revisions
No edit summary |
No edit summary |
||
| Line 1: | Line 1: | ||
[[Image:1jwr.jpg|left|200px]] | [[Image:1jwr.jpg|left|200px]] | ||
'''Crystal structure of human lysozyme at 100 K''' | {{Structure | ||
|PDB= 1jwr |SIZE=350|CAPTION= <scene name='initialview01'>1jwr</scene>, resolution 1.40Å | |||
|SITE= | |||
|LIGAND= | |||
|ACTIVITY= [http://en.wikipedia.org/wiki/Lysozyme Lysozyme], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.17 3.2.1.17] | |||
|GENE= | |||
}} | |||
'''Crystal structure of human lysozyme at 100 K''' | |||
==Overview== | ==Overview== | ||
| Line 10: | Line 19: | ||
==About this Structure== | ==About this Structure== | ||
1JWR is a [ | 1JWR is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JWR OCA]. | ||
==Reference== | ==Reference== | ||
Hydration structure of human lysozyme investigated by molecular dynamics simulation and cryogenic X-ray crystal structure analyses: on the correlation between crystal water sites, solvent density, and solvent dipole., Higo J, Nakasako M, J Comput Chem. 2002 Nov 15;23(14):1323-36. PMID:[http:// | Hydration structure of human lysozyme investigated by molecular dynamics simulation and cryogenic X-ray crystal structure analyses: on the correlation between crystal water sites, solvent density, and solvent dipole., Higo J, Nakasako M, J Comput Chem. 2002 Nov 15;23(14):1323-36. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12214315 12214315] | ||
[[Category: Homo sapiens]] | [[Category: Homo sapiens]] | ||
[[Category: Lysozyme]] | [[Category: Lysozyme]] | ||
| Line 21: | Line 30: | ||
[[Category: hydration structure]] | [[Category: hydration structure]] | ||
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 12:09:32 2008'' | ||
Revision as of 13:09, 20 March 2008
| |||||||
| , resolution 1.40Å | |||||||
|---|---|---|---|---|---|---|---|
| Activity: | Lysozyme, with EC number 3.2.1.17 | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Crystal structure of human lysozyme at 100 K
OverviewOverview
The hydration structure of human lysozyme was studied with cryogenic X-ray diffraction experiment and molecular dynamics simulations. The crystal structure analysis at a resolution of 1.4 A provided 405 crystal water molecules around the enzyme. In the simulations at 300 K, the crystal structure was immersed in explicit water molecules. We examined correlations between crystal water sites and two physical quantities calculated from the 1-ns simulation trajectories: the solvent density reflecting the time-averaged distribution of water molecules, and the solvent dipole measuring the orientational ordering of water molecules around the enzyme. The local high solvent density sites were consistent with the crystal water sites, and better correlation was observed around surface residues with smaller conformational fluctuations during the simulations. Solvent dipoles around those sites exhibited coherent and persistent ordering, indicating that the hydration water molecules at the crystal water sites were highly oriented through the interactions with hydrophilic residues. Those water molecules restrained the orientational motions of adjoining water molecules and induced a solvent dipole field, which was persistent during the simulations around the enzyme. The coherent ordering was particularly prominent in and around the active site cleft of the enzyme. Because the ordering was significant up to the third to fourth solvent layer region from the enzyme surface, the coherently ordered solvent dipoles likely contributed to the molecular recognition of the enzyme in a long-distance range. The present work may provide a new approach combining computational and the experimental studies to understand protein hydration.
DiseaseDisease
Known diseases associated with this structure: Amyloidosis, renal OMIM:[153450], Microphthalmia, syndromic 1 OMIM:[309800]
About this StructureAbout this Structure
1JWR is a Single protein structure of sequence from Homo sapiens. Full crystallographic information is available from OCA.
ReferenceReference
Hydration structure of human lysozyme investigated by molecular dynamics simulation and cryogenic X-ray crystal structure analyses: on the correlation between crystal water sites, solvent density, and solvent dipole., Higo J, Nakasako M, J Comput Chem. 2002 Nov 15;23(14):1323-36. PMID:12214315
Page seeded by OCA on Thu Mar 20 12:09:32 2008