5k1d: Difference between revisions

Latest revision as of 13:30, 1 July 2026

Crystal structure of a class C beta lactamase/compound1 complex

Structural highlights

5k1d is a 1 chain structure with sequence from Klebsiella aerogenes. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.94Å
Ligands:	5GP, CD
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

BLC10_KLEAE Class C beta-lactamase which confers resistance to penicillins and cephalosporins (PubMed:15383166). Has benzylpenicillin-, ceftazidime-, nitrocefin- and imipenem-hydrolyzing activity (PubMed:16677302, PubMed:28242658).^[1] ^[2] ^[3]

Publication Abstract from PubMed

Nucleotides were effective in inhibiting the class C beta-lactamase CMY-10. IMP was the most potent competitive inhibitor, with a Ki value of 16.2 muM. The crystal structure of CMY-10 complexed with GMP or IMP revealed that nucleotides fit into the R2 subsite of the active site with a unique vertical binding mode where the phosphate group at one terminus is deeply bound in the subsite and the base at the other terminus faces the solvent.

GMP and IMP Are Competitive Inhibitors of CMY-10, an Extended-Spectrum Class C beta-Lactamase.,Na JH, An YJ, Cha SS Antimicrob Agents Chemother. 2017 Apr 24;61(5). pii: e00098-17. doi:, 10.1128/AAC.00098-17. Print 2017 May. PMID:28242658^[4]

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

References

↑ Lee JH, Jung HI, Jung JH, Park JS, Ahn JB, Jeong SH, Jeong BC, Lee JH, Lee SH. Dissemination of transferable AmpC-type beta-lactamase (CMY-10) in a Korean hospital. Microb Drug Resist. 2004 Fall;10(3):224-30. PMID:15383166 doi:10.1089/mdr.2004.10.224
↑ Kim JY, Jung HI, An YJ, Lee JH, Kim SJ, Jeong SH, Lee KJ, Suh PG, Lee HS, Lee SH, Cha SS. Structural basis for the extended substrate spectrum of CMY-10, a plasmid-encoded class C beta-lactamase. Mol Microbiol. 2006 May;60(4):907-16. PMID:16677302 doi:10.1111/j.1365-2958.2006.05146.x
↑ Na JH, An YJ, Cha SS. GMP and IMP Are Competitive Inhibitors of CMY-10, an Extended-Spectrum Class C beta-Lactamase. Antimicrob Agents Chemother. 2017 Apr 24;61(5). pii: e00098-17. doi:, 10.1128/AAC.00098-17. Print 2017 May. PMID:28242658 doi:https://dx.doi.org/10.1128/AAC.00098-17
↑ Na JH, An YJ, Cha SS. GMP and IMP Are Competitive Inhibitors of CMY-10, an Extended-Spectrum Class C beta-Lactamase. Antimicrob Agents Chemother. 2017 Apr 24;61(5). pii: e00098-17. doi:, 10.1128/AAC.00098-17. Print 2017 May. PMID:28242658 doi:https://dx.doi.org/10.1128/AAC.00098-17

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Lee JH, Jung HI, Jung JH, Park JS, Ahn JB, Jeong SH, Jeong BC, Lee JH, Lee SH. Dissemination of transferable AmpC-type beta-lactamase (CMY-10) in a Korean hospital. Microb Drug Resist. 2004 Fall;10(3):224-30. PMID:15383166 doi:10.1089/mdr.2004.10.224

[2] Kim JY, Jung HI, An YJ, Lee JH, Kim SJ, Jeong SH, Lee KJ, Suh PG, Lee HS, Lee SH, Cha SS. Structural basis for the extended substrate spectrum of CMY-10, a plasmid-encoded class C beta-lactamase. Mol Microbiol. 2006 May;60(4):907-16. PMID:16677302 doi:10.1111/j.1365-2958.2006.05146.x

[3] Na JH, An YJ, Cha SS. GMP and IMP Are Competitive Inhibitors of CMY-10, an Extended-Spectrum Class C beta-Lactamase. Antimicrob Agents Chemother. 2017 Apr 24;61(5). pii: e00098-17. doi:, 10.1128/AAC.00098-17. Print 2017 May. PMID:28242658 doi:https://dx.doi.org/10.1128/AAC.00098-17

[4] Na JH, An YJ, Cha SS. GMP and IMP Are Competitive Inhibitors of CMY-10, an Extended-Spectrum Class C beta-Lactamase. Antimicrob Agents Chemother. 2017 Apr 24;61(5). pii: e00098-17. doi:, 10.1128/AAC.00098-17. Print 2017 May. PMID:28242658 doi:https://dx.doi.org/10.1128/AAC.00098-17

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[2]

[3]

[4]

@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 5k1d is ON HOLD  until Paper Publication
+==Crystal structure of a class C beta lactamase/compound1 complex==
+<StructureSection load='5k1d' size='340' side='right'caption='[[5k1d]], [[Resolution|resolution]] 1.94&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[5k1d]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Klebsiella_aerogenes Klebsiella aerogenes]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5K1D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5K1D FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.94&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5GP:GUANOSINE-5-MONOPHOSPHATE'>5GP</scene>, <scene name='pdbligand=CD:CADMIUM+ION'>CD</scene></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=5k1d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k1d OCA], [https://pdbe.org/5k1d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5k1d RCSB], [https://www.ebi.ac.uk/pdbsum/5k1d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5k1d ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/BLC10_KLEAE BLC10_KLEAE] Class C beta-lactamase which confers resistance to penicillins and cephalosporins (PubMed:15383166). Has benzylpenicillin-, ceftazidime-, nitrocefin- and imipenem-hydrolyzing activity (PubMed:16677302, PubMed:28242658).<ref>PMID:15383166</ref> <ref>PMID:16677302</ref> <ref>PMID:28242658</ref>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Nucleotides were effective in inhibiting the class C beta-lactamase CMY-10. IMP was the most potent competitive inhibitor, with a Ki value of 16.2 muM. The crystal structure of CMY-10 complexed with GMP or IMP revealed that nucleotides fit into the R2 subsite of the active site with a unique vertical binding mode where the phosphate group at one terminus is deeply bound in the subsite and the base at the other terminus faces the solvent.
-Authors: AN, Y.J., Na, J.H., Kim, M.K., Cha, S.S.
+GMP and IMP Are Competitive Inhibitors of CMY-10, an Extended-Spectrum Class C beta-Lactamase.,Na JH, An YJ, Cha SS Antimicrob Agents Chemother. 2017 Apr 24;61(5). pii: e00098-17. doi:, 10.1128/AAC.00098-17. Print 2017 May. PMID:28242658<ref>PMID:28242658</ref>
-Description: Crystal structure of a class C beta lactamase/compound1 complex
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
-[[Category: Na, J.H]]
+<div class="pdbe-citations 5k1d" style="background-color:#fffaf0;"></div>
-[[Category: Kim, M.K]]
-[[Category: Cha, S.S]]
+==See Also==
-[[Category: An, Y.J]]
+*[[Beta-lactamase 3D structures|Beta-lactamase 3D structures]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Klebsiella aerogenes]]
+[[Category: Large Structures]]
+[[Category: AN YJ]]
+[[Category: Cha SS]]
+[[Category: Na JH]]

5k1d: Difference between revisions

Latest revision as of 13:30, 1 July 2026

Crystal structure of a class C beta lactamase/compound1 complex

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

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