Added definition for PLP (pyridoxin-5'-phosphate) protein modification to xml file and added unit test.

pwrose · pwrose · commit e814b321955f · 2016-05-10T12:15:52.000-07:00
diff --git a/biojava-modfinder/src/main/resources/org/biojava/nbio/protmod/ptm_list.xml b/biojava-modfinder/src/main/resources/org/biojava/nbio/protmod/ptm_list.xml
@@ -13694,4 +13694,40 @@
 		<Category>attachment</Category>
 		<Keyword>glycoprotein</Keyword>
 	</Entry>
+	<Entry>
+		<Id>0430</Id>
+		<Description>A protein modification that effectively converts an L-lysine residue to N6-pyridoxal phosphate-L-lysine.</Description>
+		<SystematicName>(S)-2-amino-6-[([3-hydroxy-2-methyl-5-phosphonooxymethylpyridin-4-yl]methylidene)amino]hexanoic acid</SystematicName>
+		<CrossReference>
+			<Source>PDBCC</Source>
+			<Id>PLP</Id>
+			<Name>2-lysine(3-hydroxy-2-methyl-5-phosphonooxymethyl-pyridin-4-ylmethane)</Name>
+		</CrossReference>
+		<CrossReference>
+			<Source>RESID</Source>
+			<Id>AA0119</Id>
+			<Name>N6-pyridoxal phosphate-L-lysine</Name>
+		</CrossReference>
+		<CrossReference>
+			<Source>PSI-MOD</Source>
+			<Id>MOD:00128</Id>
+			<Name>N6-pyridoxal phosphate-L-lysine</Name>
+		</CrossReference>
+		<Condition>
+			<Component component="1">
+				<Id source="PDBCC">PLP</Id>
+			</Component>
+			<Component component="2">
+				<Id source="PDBCC">LYS</Id>
+			</Component>
+			<Bond>
+				<Atom component="1">C4A</Atom>
+				<Atom component="2">NZ</Atom>
+			</Bond>
+		</Condition>
+		<Occurrence>natural</Occurrence>
+		<Category>attachment</Category>
+		<Keyword>phosphoprotein</Keyword>
+		<Keyword>pyridoxal phosphate</Keyword>
+	</Entry>
 </ProteinModifications>
diff --git a/biojava-modfinder/src/test/java/org/biojava/nbio/protmod/structure/ProteinModificationParserTest.java b/biojava-modfinder/src/test/java/org/biojava/nbio/protmod/structure/ProteinModificationParserTest.java
@@ -64,10 +64,12 @@ public static String[][] setUpShortTest() {
 //				{"1ZNF", "AA0053"}, // ACE on THR
 				{"1MCC", "AA0045"}, // ACE on GLU
 				{"1SCY", "AA0089"}, // NH2 on HIS
+				{"5HNE", "AA0119"}, // PLP on LYS
 
 				// Modified resdiues
 				{"1UIS", "AA0183"}, // NRQ
 				{"3MVJ", "AA0037"}, // SEP
+				{"5EUN", "AA0119"}, // LLP
 
 				// remediation changed 1DOJ...
 				//{"1DOJ", "AA0065"}, // MEA
