1ic6
From Proteopedia
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|PDB= 1ic6 |SIZE=350|CAPTION= <scene name='initialview01'>1ic6</scene>, resolution 0.98Å | |PDB= 1ic6 |SIZE=350|CAPTION= <scene name='initialview01'>1ic6</scene>, resolution 0.98Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene> | + | |LIGAND= <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=NO3:NITRATE+ION'>NO3</scene> |
| - | |ACTIVITY= [http://en.wikipedia.org/wiki/Peptidase_K Peptidase K], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.64 3.4.21.64] | + | |ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Peptidase_K Peptidase K], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.64 3.4.21.64] </span> |
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY= | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ic6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ic6 OCA], [http://www.ebi.ac.uk/pdbsum/1ic6 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1ic6 RCSB]</span> | ||
}} | }} | ||
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[[Category: Perbandt, M.]] | [[Category: Perbandt, M.]] | ||
[[Category: Singh, T P.]] | [[Category: Singh, T P.]] | ||
| - | [[Category: CA]] | ||
| - | [[Category: NO3]] | ||
[[Category: proteinase k]] | [[Category: proteinase k]] | ||
[[Category: serine protease]] | [[Category: serine protease]] | ||
[[Category: structure]] | [[Category: structure]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 21:17:39 2008'' |
Revision as of 18:17, 30 March 2008
| |||||||
| , resolution 0.98Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , | ||||||
| Activity: | Peptidase K, with EC number 3.4.21.64 | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
STRUCTURE OF A SERINE PROTEASE PROTEINASE K FROM TRITIRACHIUM ALBUM LIMBER AT 0.98 A RESOLUTION
Overview
X-ray diffraction data at atomic resolution to 0.98 A with 136 380 observed unique reflections were collected using a high quality proteinase K crystals grown under microgravity conditions and cryocooled. The structure has been refined anisotropically with REFMAC and SHELX-97 with R-factors of 11.4 and 12.8%, and R(free)-factors of 12.4 and 13.5%, respectively. The refined model coordinates have an overall rms shifts of 0.23 A relative to the same structure determined at room temperature at 1.5 A resolution. Several regions of the main chain and the side chains, which were not observed earlier have been seen more clearly. For example, amino acid 207, which was reported earlier as Ser has been clearly identified as Asp. Furthermore, side-chain disorders of 8 of 279 residues in the polypeptide have been identified. Hydrogen atoms appear as significant peaks in the F(o) - F(c) difference electron density map accounting for an estimated 46% of all hydrogen atoms at 2sigma level. Furthermore, the carbon, nitrogen, and oxygen atoms can be differentiated clearly in the electron density maps. Hydrogen bonds are clearly identified in the serine protease catalytic triad (Ser-His-Asp). Furthermore, electron density is observed for an unusual, short hydrogen bond between aspartic acid and histidine in the catalytic triad. The short hydrogen bond, designated "catalytic hydrogen bond", occurs as part of an elaborate hydrogen bond network, involving Asp of the catalytic triad. Though unusual, these features seem to be conserved in other serine proteases. Finally there are clear electron density peaks for the hydrogen atoms associated with the Ogamma of Ser 224 and Ndelta1 of His 69.
About this Structure
1IC6 is a Single protein structure of sequence from Engyodontium album. Full crystallographic information is available from OCA.
Reference
Structure of a serine protease proteinase K from Tritirachium album limber at 0.98 A resolution., Betzel C, Gourinath S, Kumar P, Kaur P, Perbandt M, Eschenburg S, Singh TP, Biochemistry. 2001 Mar 13;40(10):3080-8. PMID:11258922
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