This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.

1b3g

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Revision as of 10:39, 19 May 2021

OLIGO-PEPTIDE BINDING PROTEIN (OPPA) COMPLEXED WITH KIK

Structural highlights

1b3g is a 2 chain structure. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
Related:	1b3f
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[OPPA_SALTY] This protein is a component of the oligopeptide permease, a binding protein-dependent transport system, it binds peptides up to five amino acids long with high affinity.

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

Isothermal titration calorimetry has been used to study the binding of 20 different peptides to the peptide binding protein OppA, and the crystal structures of the ligand complexes have been refined. This periplasmic binding protein, part of the oligopeptide permease system of Gram negative bacteria, has evolved to bind and enclose small peptides of widely varying sequences. The peptides used in this study have the sequence Lys-X-Lys, where X is any of the 20 commonly occurring amino acids. The various side-chains found at position 2 on the ligand fit into a hydrated pocket. The majority of side-chains are restrained to particular conformations within the pocket. Water molecules act as flexible adapters, matching the hydrogen-bonding requirements of the protein and ligand and shielding charges on the buried ligand. This use of water by OppA to broaden the repertoire of its binding site is not unique, but contrasts sharply with other proteins which use water to help bind ligands highly selectively. Predicting the thermodynamics of binding from the structure of the complexes is highly complicated by the influence of water on the system.

Crystallographic and calorimetric analysis of peptide binding to OppA protein.,Sleigh SH, Seavers PR, Wilkinson AJ, Ladbury JE, Tame JR J Mol Biol. 1999 Aug 13;291(2):393-415. PMID:10438628^[1]

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

References

↑ Sleigh SH, Seavers PR, Wilkinson AJ, Ladbury JE, Tame JR. Crystallographic and calorimetric analysis of peptide binding to OppA protein. J Mol Biol. 1999 Aug 13;291(2):393-415. PMID:10438628 doi:10.1006/jmbi.1999.2929

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/1b3g"

Categories: Large Structures | Tame, J R.H | Wilkinson, A J | Peptide binding protein | Peptide transport

@@ Line 3: / Line 3: @@
 <StructureSection load='1b3g' size='340' side='right'caption='[[1b3g]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1b3g]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1B3G OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1B3G FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1b3g]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1B3G OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1B3G FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=IUM:URANYL+(VI)+ION'>IUM</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=IUM:URANYL+(VI)+ION'>IUM</scene></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1b3f|1b3f]]</td></tr>
+<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1b3f|1b3f]]</div></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=1b3g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1b3g OCA], [http://pdbe.org/1b3g PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1b3g RCSB], [http://www.ebi.ac.uk/pdbsum/1b3g PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1b3g ProSAT]</span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1b3g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1b3g OCA], [https://pdbe.org/1b3g PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1b3g RCSB], [https://www.ebi.ac.uk/pdbsum/1b3g PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1b3g ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/OPPA_SALTY OPPA_SALTY]] This protein is a component of the oligopeptide permease, a binding protein-dependent transport system, it binds peptides up to five amino acids long with high affinity.
+[[https://www.uniprot.org/uniprot/OPPA_SALTY OPPA_SALTY]] This protein is a component of the oligopeptide permease, a binding protein-dependent transport system, it binds peptides up to five amino acids long with high affinity.
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 31: / Line 31: @@
 ==See Also==
-*[[Oligopeptide-binding protein|Oligopeptide-binding protein]]
+*[[ABC transporter 3D structures|ABC transporter 3D structures]]
 == References ==
 <references/>

1b3g

From Proteopedia

Revision as of 10:39, 19 May 2021

OLIGO-PEPTIDE BINDING PROTEIN (OPPA) COMPLEXED WITH KIK

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox