1dy5

From Proteopedia

(Difference between revisions)

Revision as of 04:02, 30 August 2017

Deamidated derivative of bovine pancreatic ribonuclease

Structural highlights

1dy5 is a 2 chain structure with sequence from Bos taurus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	, ,
NonStd Res:
Related:	1ssb, 1w4q, 1afu, 1c0b, 6rat, 1ymr, 1o0o, 8rsa, 5rsa, 7rat, 1rno, 2w5l, 1izq, 1eid, 1cjq, 1eos, 1rnn, 1j82, 1qhc, 1ymw, 1f0v, 1afk, 1o0h, 1jn4, 1rnq, 1rnm, 1rbf, 1z3m, 1rnx, 1rob, 1rbn, 1rbx, 1eow, 1rbi, 7rsa, 1rbj, 1dfj, 1rsm, 1kf5, 1xps, 1rat, 1fev, 2aas, 1j80, 1rhb, 1rpg, 1fs3, 1b6v, 3srn, 1z6s, 1kf8, 1rtb, 4rsk, 1bzq, 9rsa, 1bel, 1kf4, 1kf7, 1rbw, 9rat, 1eie, 1rpf, 1o0m, 1c8w, 1rnc, 1rca, 1jvt, 1c0c, 3rsd, 1xpt, 1rbb, 2blz, 3rsp, 1ssc, 8rat, 2apq, 1w4o, 1j7z, 1rbd, 1rnz, 1jvv, 1rar, 1z3l, 1kf3, 1aqp, 2w5m, 1rbh, 1rbg, 1o0n, 3rsk, 1js0, 1ssa, 1cjr, 1eic, 1d5d, 1ymn, 1j81, 1rnw, 2w5k, 1rph, 2rns, 1rta, 1rnu, 1rny, 1z3p, 1gv7, 1rcn, 1rnv, 4rat, 1w4p, 4rsd, 1a5p, 1wbu, 1rha, 1ras, 2blp, 1kf2, 1rnd, 1d5h, 1srn, 1d5e, 2rat, 1izp, 2w5g, 1o0f, 1izr, 1c9x, 2rln, 4srn, 1c9v, 5rat, 1u1b, 1ruv, 2w5i, 1rbc, 1afl, 1z6d, 1rbe, 1a5q, 1kh8, 1lsq, 1jvu, 1a2w, 3rat, 3rn3
Activity:	Pancreatic ribonuclease, with EC number 3.1.27.5
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[RNAS1_BOVIN] Endonuclease that catalyzes the cleavage of RNA on the 3' side of pyrimidine nucleotides. Acts on single stranded and double stranded RNA.^[1]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

Crystals of the deamidated form of bovine pancreatic ribonuclease which contains an isoaspartyl residue in position 67 diffract to 0. 87 A at 100 K. We have refined the crystallographic model using anisotropic displacement parameters for all atoms to a conventional crystallographic residual R=0.101 for all observed reflections in the resolution range 61.0-0.87 A. The ratio observations/parameters is 7.2 for the final model. This structure represents one of the highest resolution protein structures to date and interestingly, it is the only example containing more than one molecule in the asymmetric unit with a resolution better than 1.0 A. The non-crystallographic symmetry has been used as a validation check of the geometrical parameters and it has allowed an estimate for an upper limit of errors associated with this high resolution model. In the present structure it was possible to obtain a more accurate picture of the active site whose electron density was not clearly interpretable in the previous 1.9 A resolution structure. In particular, the P1 site is alternatively occupied either by a sulphate anion or by a water molecule network. Most of hydrogen atoms were visible in the electron density maps, including those involved in C(alpha)-H(alpha).O interactions. Analysis of protein-solvent interactions has revealed the occurrence of an extensive cluster of water molecules, predominantly arranged in pentagonal fused rings and surrounding hydrophobic moiety of side-chains. Finally, in spite of the limited sample of residues, we have detected a clear dependence of backbone N-C(alpha)-C angle on residue conformation. This correlation can be fruitfully used as a valuable tool in protein structure validation.

The ultrahigh resolution crystal structure of ribonuclease A containing an isoaspartyl residue: hydration and sterochemical analysis.,Esposito L, Vitagliano L, Sica F, Sorrentino G, Zagari A, Mazzarella L J Mol Biol. 2000 Mar 31;297(3):713-32. PMID:10731423^[2]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ delCardayre SB, Ribo M, Yokel EM, Quirk DJ, Rutter WJ, Raines RT. Engineering ribonuclease A: production, purification and characterization of wild-type enzyme and mutants at Gln11. Protein Eng. 1995 Mar;8(3):261-73. PMID:7479688
↑ Esposito L, Vitagliano L, Sica F, Sorrentino G, Zagari A, Mazzarella L. The ultrahigh resolution crystal structure of ribonuclease A containing an isoaspartyl residue: hydration and sterochemical analysis. J Mol Biol. 2000 Mar 31;297(3):713-32. PMID:10731423 doi:10.1006/jmbi.2000.3597

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1dy5"

@@ Line 1: / Line 1: @@
-==DEAMIDATED DERIVATIVE OF BOVINE PANCREATIC RIBONUCLEASE==
+==Deamidated derivative of bovine pancreatic ribonuclease==
 <StructureSection load='1dy5' size='340' side='right' caption='[[1dy5]], [[Resolution|resolution]] 0.87&Aring;' scene=''>
 == Structural highlights ==
@@ Line 7: / Line 8: @@
 <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1ssb|1ssb]], [[1w4q|1w4q]], [[1afu|1afu]], [[1c0b|1c0b]], [[6rat|6rat]], [[1ymr|1ymr]], [[1o0o|1o0o]], [[8rsa|8rsa]], [[5rsa|5rsa]], [[7rat|7rat]], [[1rno|1rno]], [[2w5l|2w5l]], [[1izq|1izq]], [[1eid|1eid]], [[1cjq|1cjq]], [[1eos|1eos]], [[1rnn|1rnn]], [[1j82|1j82]], [[1qhc|1qhc]], [[1ymw|1ymw]], [[1f0v|1f0v]], [[1afk|1afk]], [[1o0h|1o0h]], [[1jn4|1jn4]], [[1rnq|1rnq]], [[1rnm|1rnm]], [[1rbf|1rbf]], [[1z3m|1z3m]], [[1rnx|1rnx]], [[1rob|1rob]], [[1rbn|1rbn]], [[1rbx|1rbx]], [[1eow|1eow]], [[1rbi|1rbi]], [[7rsa|7rsa]], [[1rbj|1rbj]], [[1dfj|1dfj]], [[1rsm|1rsm]], [[1kf5|1kf5]], [[1xps|1xps]], [[1rat|1rat]], [[1fev|1fev]], [[2aas|2aas]], [[1j80|1j80]], [[1rhb|1rhb]], [[1rpg|1rpg]], [[1fs3|1fs3]], [[1b6v|1b6v]], [[3srn|3srn]], [[1z6s|1z6s]], [[1kf8|1kf8]], [[1rtb|1rtb]], [[4rsk|4rsk]], [[1bzq|1bzq]], [[9rsa|9rsa]], [[1bel|1bel]], [[1kf4|1kf4]], [[1kf7|1kf7]], [[1rbw|1rbw]], [[9rat|9rat]], [[1eie|1eie]], [[1rpf|1rpf]], [[1o0m|1o0m]], [[1c8w|1c8w]], [[1rnc|1rnc]], [[1rca|1rca]], [[1jvt|1jvt]], [[1c0c|1c0c]], [[3rsd|3rsd]], [[1xpt|1xpt]], [[1rbb|1rbb]], [[2blz|2blz]], [[3rsp|3rsp]], [[1ssc|1ssc]], [[8rat|8rat]], [[2apq|2apq]], [[1w4o|1w4o]], [[1j7z|1j7z]], [[1rbd|1rbd]], [[1rnz|1rnz]], [[1jvv|1jvv]], [[1rar|1rar]], [[1z3l|1z3l]], [[1kf3|1kf3]], [[1aqp|1aqp]], [[2w5m|2w5m]], [[1rbh|1rbh]], [[1rbg|1rbg]], [[1o0n|1o0n]], [[3rsk|3rsk]], [[1js0|1js0]], [[1ssa|1ssa]], [[1cjr|1cjr]], [[1eic|1eic]], [[1d5d|1d5d]], [[1ymn|1ymn]], [[1j81|1j81]], [[1rnw|1rnw]], [[2w5k|2w5k]], [[1rph|1rph]], [[2rns|2rns]], [[1rta|1rta]], [[1rnu|1rnu]], [[1rny|1rny]], [[1z3p|1z3p]], [[1gv7|1gv7]], [[1rcn|1rcn]], [[1rnv|1rnv]], [[4rat|4rat]], [[1w4p|1w4p]], [[4rsd|4rsd]], [[1a5p|1a5p]], [[1wbu|1wbu]], [[1rha|1rha]], [[1ras|1ras]], [[2blp|2blp]], [[1kf2|1kf2]], [[1rnd|1rnd]], [[1d5h|1d5h]], [[1srn|1srn]], [[1d5e|1d5e]], [[2rat|2rat]], [[1izp|1izp]], [[2w5g|2w5g]], [[1o0f|1o0f]], [[1izr|1izr]], [[1c9x|1c9x]], [[2rln|2rln]], [[4srn|4srn]], [[1c9v|1c9v]], [[5rat|5rat]], [[1u1b|1u1b]], [[1ruv|1ruv]], [[2w5i|2w5i]], [[1rbc|1rbc]], [[1afl|1afl]], [[1z6d|1z6d]], [[1rbe|1rbe]], [[1a5q|1a5q]], [[1kh8|1kh8]], [[1lsq|1lsq]], [[1jvu|1jvu]], [[1a2w|1a2w]], [[3rat|3rat]], [[3rn3|3rn3]]</td></tr>
 <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Pancreatic_ribonuclease Pancreatic ribonuclease], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.27.5 3.1.27.5] </span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1dy5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dy5 OCA], [http://pdbe.org/1dy5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1dy5 RCSB], [http://www.ebi.ac.uk/pdbsum/1dy5 PDBsum]</span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1dy5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dy5 OCA], [http://pdbe.org/1dy5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1dy5 RCSB], [http://www.ebi.ac.uk/pdbsum/1dy5 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1dy5 ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 19: / Line 20: @@
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
-</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
+</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1dy5 ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">

1dy5

From Proteopedia

Revision as of 04:02, 30 August 2017

Deamidated derivative of bovine pancreatic ribonuclease

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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