4UFW - JenaLib

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Biological Unit 3 (Jmol Viewer)

Title :   PLASMODIUM VIVAX N-MYRISTOYLTRANSFERASE IN COMPLEX WITH A PYRIDYL INHIBITOR (COMPOUND 22)

Authors :   Z. Yu, J. A. Brannigan, K. Rangachari, W. P. Heal, A. J. Wilkinson, A. A. H E. W. Tate, R. J. Leatherbarrow

Date :   19 Mar 15 (Deposition) - 03 Feb 16 (Release) - 20 Apr 16 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.50

Chains :   Asym. Unit : A,B,C
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: C  (1x)

Keywords :   Transferase, Myristoylation, Malaria, Inhibitor, Pyridyl (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Z. Yu, J. A. Brannigan, K. Rangachari, W. P. Heal, A. J. Wilkinson, A. A. Holder, R. J. Leatherbarrow, E. W. Tate
Discovery Of Pyridyl-Based Inhibitors Of Plasmodium Falciparum N-Myristoyltransferase
Medchemcomm V. 6 1767 2015
PubMed-ID: 26962430 | Reference-DOI: 10.1039/C5MD00242G

Molecule 1 - GLYCYLPEPTIDE N-TETRADECANOYLTRANSFERASE
	Chains	:	A, B, C
	EC Number	:	2.3.1.97
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28 DERIVATIVE
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Variant	:	PLYSS
	Fragment	:	RESIDUES 27-410
	Organism Common	:	MALARIA PARASITE P. VIVAX
	Organism Scientific	:	PLASMODIUM VIVAX
	Organism Taxid	:	5855

		1	2	3
Asymmetric Unit	:	A	B	C
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (1x)	:			C

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (6, 16)

No.	Name	Count	Type	Full Name
1	7Y6	3	Ligand/Ion	4-CHLORANYL-N-[2-(3-METHOXYPHENYL)ETHANIMIDOYL]-2-PIPERIDIN-4-YLOXY-BENZAMIDE
2	CL	3	Ligand/Ion	CHLORIDE ION
3	DMS	3	Ligand/Ion	DIMETHYL SULFOXIDE
4	MG	3	Ligand/Ion	MAGNESIUM ION
5	NHW	3	Ligand/Ion	2-OXOPENTADECYL-COA
6	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 1 (4, 4)

No.	Name	Count	Type	Full Name
1	7Y6	1	Ligand/Ion	4-CHLORANYL-N-[2-(3-METHOXYPHENYL)ETHANIMIDOYL]-2-PIPERIDIN-4-YLOXY-BENZAMIDE
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	DMS	1	Ligand/Ion	DIMETHYL SULFOXIDE
4	MG	-1	Ligand/Ion	MAGNESIUM ION
5	NHW	1	Ligand/Ion	2-OXOPENTADECYL-COA
6	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 2 (3, 3)

No.	Name	Count	Type	Full Name
1	7Y6	1	Ligand/Ion	4-CHLORANYL-N-[2-(3-METHOXYPHENYL)ETHANIMIDOYL]-2-PIPERIDIN-4-YLOXY-BENZAMIDE
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	DMS	1	Ligand/Ion	DIMETHYL SULFOXIDE
4	MG	-1	Ligand/Ion	MAGNESIUM ION
5	NHW	1	Ligand/Ion	2-OXOPENTADECYL-COA
6	SO4	-1	Ligand/Ion	SULFATE ION

Biological Unit 3 (3, 3)

No.	Name	Count	Type	Full Name
1	7Y6	1	Ligand/Ion	4-CHLORANYL-N-[2-(3-METHOXYPHENYL)ETHANIMIDOYL]-2-PIPERIDIN-4-YLOXY-BENZAMIDE
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	DMS	1	Ligand/Ion	DIMETHYL SULFOXIDE
4	MG	-1	Ligand/Ion	MAGNESIUM ION
5	NHW	1	Ligand/Ion	2-OXOPENTADECYL-COA
6	SO4	-1	Ligand/Ion	SULFATE ION

Asymmetric Unit (16, 16)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	TYR A:28 , LYS A:29 , PHE A:30 , TRP A:31 , ASN A:94 , TYR A:95 , VAL A:96 , ASN A:161 , PHE A:162 , LEU A:163 , CYS A:164 , VAL A:165 , ARG A:170 , SER A:171 , LYS A:172 , ARG A:173 , LEU A:174 , ALA A:175 , PRO A:176 , THR A:183 , ILE A:186 , TRP A:192 , GLN A:193 , TYR A:196 , THR A:197 , LEU A:202 , TYR A:393 , MG A:1413 , HOH A:2001 , HOH A:2003 , HOH A:2240 , HOH A:2248 , HOH A:2249 , HOH A:2468 , HOH A:2469 , HOH A:2470 , HOH A:2471 , HOH A:2472 , HOH A:2473	BINDING SITE FOR RESIDUE NHW A1000
02	AC2	SOFTWARE	VAL A:96 , GLU A:97 , ASP A:98 , PHE A:103 , PHE A:105 , TYR A:107 , TYR A:211 , TYR A:315 , LEU A:317 , SER A:319 , TYR A:334 , ASN A:365 , ALA A:366 , LEU A:409 , LEU A:410 , HOH A:2281 , HOH A:2412 , HOH A:2467 , HOH A:2474	BINDING SITE FOR RESIDUE 7Y6 A1411
03	AC3	SOFTWARE	ARG A:210 , LYS A:373 , ARG B:210	BINDING SITE FOR RESIDUE SO4 A1412
04	AC4	SOFTWARE	LEU A:169 , SER A:171 , LYS A:172 , ARG A:173 , LEU A:174 , NHW A:1000	BINDING SITE FOR RESIDUE MG A1413
05	AC5	SOFTWARE	LYS A:180 , THR A:247 , LEU A:248 , ARG A:358	BINDING SITE FOR RESIDUE CL A1414
06	AC6	SOFTWARE	GLU A:159 , PHE A:281 , TRP A:289 , HOH A:2413	BINDING SITE FOR RESIDUE DMS A1415
07	AC7	SOFTWARE	TYR B:28 , LYS B:29 , PHE B:30 , TRP B:31 , ASN B:94 , TYR B:95 , VAL B:96 , ASN B:161 , PHE B:162 , LEU B:163 , CYS B:164 , VAL B:165 , ARG B:170 , SER B:171 , LYS B:172 , ARG B:173 , LEU B:174 , ALA B:175 , PRO B:176 , THR B:183 , ILE B:186 , ASN B:187 , TRP B:192 , GLN B:193 , ALA B:194 , TYR B:196 , THR B:197 , LEU B:202 , TYR B:393 , MG B:1412 , HOH B:2002 , HOH B:2003 , HOH B:2200 , HOH B:2205 , HOH B:2206 , HOH B:2398 , HOH B:2399 , HOH B:2400 , HOH B:2401 , HOH B:2402 , HOH B:2403	BINDING SITE FOR RESIDUE NHW B1000
08	AC8	SOFTWARE	VAL B:96 , GLU B:97 , ASP B:98 , PHE B:103 , PHE B:105 , TYR B:107 , TYR B:211 , TYR B:315 , LEU B:317 , SER B:319 , TYR B:334 , ASN B:365 , ALA B:366 , LEU B:367 , LEU B:409 , LEU B:410 , HOH B:2125 , HOH B:2356 , HOH B:2404	BINDING SITE FOR RESIDUE 7Y6 B1411
09	AC9	SOFTWARE	LEU B:169 , SER B:171 , LYS B:172 , ARG B:173 , LEU B:174 , NHW B:1000	BINDING SITE FOR RESIDUE MG B1412
10	BC1	SOFTWARE	TYR B:65 , LYS B:180 , THR B:247 , LEU B:248 , ARG B:358 , HOH B:2286	BINDING SITE FOR RESIDUE CL B1413
11	BC2	SOFTWARE	GLU B:159 , PHE B:281 , TRP B:289 , HOH B:2358	BINDING SITE FOR RESIDUE DMS B1414
12	BC3	SOFTWARE	ASP C:27 , TYR C:28 , LYS C:29 , PHE C:30 , TRP C:31 , ASN C:94 , TYR C:95 , VAL C:96 , ASN C:161 , PHE C:162 , LEU C:163 , CYS C:164 , VAL C:165 , ARG C:170 , SER C:171 , LYS C:172 , ARG C:173 , LEU C:174 , ALA C:175 , PRO C:176 , THR C:183 , ILE C:186 , TRP C:192 , GLN C:193 , THR C:197 , LEU C:202 , TYR C:393 , MG C:1412 , HOH C:2001 , HOH C:2176 , HOH C:2181 , HOH C:2357 , HOH C:2358 , HOH C:2359 , HOH C:2360 , HOH C:2361 , HOH C:2362	BINDING SITE FOR RESIDUE NHW C1000
13	BC4	SOFTWARE	VAL C:96 , GLU C:97 , ASP C:98 , PHE C:103 , PHE C:105 , TYR C:107 , TYR C:211 , PHE C:226 , TYR C:315 , LEU C:317 , SER C:319 , TYR C:334 , ALA C:366 , LEU C:410 , HOH C:2304	BINDING SITE FOR RESIDUE 7Y6 C1411
14	BC5	SOFTWARE	LEU C:169 , SER C:171 , LYS C:172 , ARG C:173 , LEU C:174 , NHW C:1000	BINDING SITE FOR RESIDUE MG C1412
15	BC6	SOFTWARE	LYS C:180 , THR C:247 , LEU C:248 , ARG C:358	BINDING SITE FOR RESIDUE CL C1413
16	BC7	SOFTWARE	GLU C:159 , PHE C:281 , TRP C:289 , HOH C:2305	BINDING SITE FOR RESIDUE DMS C1414

(no "SS Bond" information available for 4UFW)

Asymmetric Unit

No.	Residues
1	Pro A:203	-	Lys A:204
2	Pro B:203	-	Lys B:204
3	Pro C:203	-	Lys C:204

(no "SAP(SNP)/Variant" information available for 4UFW)

(no "PROSITE Motif" information available for 4UFW)

(no "Exon" information available for 4UFW)

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:385
                                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhh.............ee......hhhhh..........eeeee....hhhhhhhhhhhhhhhh.......eee..hhhhhhhhhh....hhh.eeeeee....eeeeeeeeeeeeeee..eeeeeeeeeeeee.hhhh..hhhhhhhhhhhhhhhh....eeeeee........eeeeeeeee.hhhhhhhh.........hhhhhhhhh...........ee.hhhhhhhhhhhhhhhhh...eee..hhhhhhhhhh.....eeeeeeee..eeeeeeeeee..eee.......ee.eeee...ee...hhhhhhhhhhhhhhhh...eeeee...hhhhhh.....eeeeeeeeeeee..ee...hhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ufw A  26 MDYKFWYTQPVPKINDEFNESVNEPFISDNKVEDVRKDEYKLPPGYSWYVCDVKDEKDRSEIYTLLTDNYVEDDDNIFRFNYSAEFLLWALTSPNYLKTWHIGVKYDASNKLIGFISAIPTDICIHKRTIKMAEVNFLCVHKTLRSKRLAPVLIKEITRRINLENIWQAIYTAGVYLPKPVSDARYYHRSINVKKLIEIGFSSLNSRLTMSRAIKLYRVEDTLNIKNMRLMKKKDVEGVHKLLGSYLEQFNLYAVFTKEEIAHWFLPIENVIYTYVNEENGKIKDMISFYSLPSQILGNDKYSTLNAAYSFYNVTTTATFKQLMQDAILLAKRNNFDVFNALEVMQNKSVFEDLKFGEGDGSLKYYLYNWKCASFAPAHVGIVLL 410
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405

Chain B from PDB  Type:PROTEIN  Length:385
                                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhh.............ee......hhhhh..........eeeee....hhhhhhhhhhhhhhhh.......eee..hhhhhhhhhh....hhh.eeeeee....eeeeeeeeeeeeeee..eeeeeeeeeeeee.hhhh..hhhhhhhhhhhhhhhh.....eeeee........eeeeeeeee.hhhhhhhh.........hhhhhhhhhh..........ee.hhhhhhhhhhhhhhhhh...eee..hhhhhhhhhh.....eeeeeeee..eeeeeeeeee..eee.......ee.eeee...ee...hhhhhhhhhhhhhhhh...eeeee...hhhhhh.....eeeeeeeeeeee..ee...hhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ufw B  26 MDYKFWYTQPVPKINDEFNESVNEPFISDNKVEDVRKDEYKLPPGYSWYVCDVKDEKDRSEIYTLLTDNYVEDDDNIFRFNYSAEFLLWALTSPNYLKTWHIGVKYDASNKLIGFISAIPTDICIHKRTIKMAEVNFLCVHKTLRSKRLAPVLIKEITRRINLENIWQAIYTAGVYLPKPVSDARYYHRSINVKKLIEIGFSSLNSRLTMSRAIKLYRVEDTLNIKNMRLMKKKDVEGVHKLLGSYLEQFNLYAVFTKEEIAHWFLPIENVIYTYVNEENGKIKDMISFYSLPSQILGNDKYSTLNAAYSFYNVTTTATFKQLMQDAILLAKRNNFDVFNALEVMQNKSVFEDLKFGEGDGSLKYYLYNWKCASFAPAHVGIVLL 410
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405

Chain C from PDB  Type:PROTEIN  Length:367
                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhh.............ee......hhhhh..........eeeee....hhhhhhhhhhhhhhhh.......eee..hhhhhhhhhh....hhh.eeeeee.....eeeeeeeeeeeeee..eeeeeeeeeeeee.hhhh..hhhhhhhhhhhhhhhh....eeeeee........eeeeeeeee.hhhhhhhh............ee.hhhhhhhhhhhhhhhhh...eee..hhhhhhhhhh.....eeeeeeee..eeeeeeeeee..eee.......ee.eeee...ee...hhhhhhhhhhhhhhhh...eeeee...hhhhhh.....eeeeeeeeeeee..ee...hhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ufw C  27 DYKFWYTQPVPKINDEFNESVNEPFISDNKVEDVRKDEYKLPPGYSWYVCDVKDEKDRSEIYTLLTDNYVEDDDNIFRFNYSAEFLLWALTSPNYLKTWHIGVKYDASNKLIGFISAIPTDICIHKRTIKMAEVNFLCVHKTLRSKRLAPVLIKEITRRINLENIWQAIYTAGVYLPKPVSDARYYHRSINVKKLIEIGFVEDTLNIKNMRLMKKKDVEGVHKLLGSYLEQFNLYAVFTKEEIAHWFLPIENVIYTYVNEENGKIKDMISFYSLPSQILGNDKYSTLNAAYSFYNVTTTATFKQLMQDAILLAKRNNFDVFNALEVMQNKSVFEDLKFGEGDGSLKYYLYNWKCASFAPAHVGIVLL 410
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226|      253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       
                                                                                                                                                                                                                                 226|                                                                                                                                                                      
                                                                                                                                                                                                                                  244

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	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

(no "SCOP Domain" information available for 4UFW)

(no "CATH Domain" information available for 4UFW)

(no "Pfam Domain" information available for 4UFW)

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Asymmetric Unit
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	Cis Peptide Bonds
		Pro A:203 - Lys A:204	[ RasMol ]
		Pro B:203 - Lys B:204	[ RasMol ]
		Pro C:203 - Lys C:204	[ RasMol ]

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	4ufw
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4ufv	PLASMODIUM VIVAX N-MYRISTOYLTRANSFERASE IN COMPLEX WITH A PYRIDYL INHIBITOR (COMPOUND 19)
4ufx	PLASMODIUM VIVAX N-MYRISTOYLTRANSFERASE IN COMPLEX WITH A PYRIDYL INHIBITOR (COMPOUND 20)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (6, 16)

Sites (16, 16)

SS Bonds (0, 0)

Cis Peptide Bonds (3, 3)

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