1b4z

From Proteopedia

(Difference between revisions)

Revision as of 15:04, 2 June 2021

OLIGO-PEPTIDE BINDING PROTEIN (OPPA) COMPLEXED WITH KDK

Structural highlights

1b4z is a 2 chain structure. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	,
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/1b4z"

@@ Line 3: / Line 3: @@
 <StructureSection load='1b4z' size='340' side='right'caption='[[1b4z]], [[Resolution|resolution]] 1.75&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1b4z]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1B4Z OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1B4Z FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1b4z]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1B4Z OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1B4Z FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <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=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=IUM:URANYL+(VI)+ION'>IUM</scene></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=1b4z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1b4z OCA], [http://pdbe.org/1b4z PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1b4z RCSB], [http://www.ebi.ac.uk/pdbsum/1b4z PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1b4z 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=1b4z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1b4z OCA], [https://pdbe.org/1b4z PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1b4z RCSB], [https://www.ebi.ac.uk/pdbsum/1b4z PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1b4z 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 30: / Line 30: @@
 ==See Also==
-*[[Oligopeptide-binding protein|Oligopeptide-binding protein]]
+*[[ABC transporter 3D structures|ABC transporter 3D structures]]
 == References ==
 <references/>

1b4z

From Proteopedia

Revision as of 15:04, 2 June 2021

OLIGO-PEPTIDE BINDING PROTEIN (OPPA) COMPLEXED WITH KDK

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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