Isopeptide bond: Difference between revisions
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==PDB KEYWDS and LINK Records== | ==PDB KEYWDS and LINK Records== | ||
Structures containing isopeptide bonds usually have "ISOPEPTIDE BOND" in their PDB file KEYWDS record, and sometimes have LINK records (or _struct_conn in their [[Atomic coordinate file|mmCIF]] files) | Structures containing isopeptide bonds usually have "ISOPEPTIDE BOND" in their PDB file KEYWDS record, and sometimes have LINK records (or _struct_conn in their [[Atomic coordinate file|mmCIF]] files) specifying the isopeptide-bonded residues. Here are the relevant LINK records from [[3htl]]:<pre> | ||
LINK NZ LYS X 199 CG ASN X 321 1555 1555 1.43 | LINK NZ LYS X 199 CG ASN X 321 1555 1555 1.43 | ||
LINK NZ LYS X 363 CG ASN X 482 1555 1555 1.55</pre> | LINK NZ LYS X 363 CG ASN X 482 1555 1555 1.55</pre> | ||
Note that link records involving MSE ([[selenomethionine]]) generally signify nothing more than MSE being part of a polypeptide chain, but are required because the HETATM MSE residue is covalently linked to the adjacent standard amino acids. | Note that link records involving MSE ([[selenomethionine]]) generally signify nothing more than MSE being part of a polypeptide chain, but are required because the HETATM MSE residue is covalently linked to the adjacent standard amino acids. | ||
===Unspecified Isopeptide Bonds=== | |||
Some structures that contain isopeptide bonds lack LINK/_struct_conn records describing these bonds. For example, [[1fma]] has an isopeptide bond between Lys118 chain E, and the carboxy-terminal Gly81 in chain D; [[5jqf]] has an isopepide bond between Asp9 and NH<sub>3</sub> on the amino-terminal Gly1. Neither has LINK /_struct_conn records for their isopeptide bonds. | Some structures that contain isopeptide bonds lack LINK/_struct_conn records describing these bonds. For example, [[1fma]] has an isopeptide bond between Lys118 chain E, and the carboxy-terminal Gly81 in chain D; [[5jqf]] has an isopepide bond between Asp9 and NH<sub>3</sub> on the amino-terminal Gly1. Neither has LINK /_struct_conn records for their isopeptide bonds. | ||
