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(-) Description

Title :  PLASMODIUM VIVAX N-MYRISTOYLTRANSFERASE IN COMPLEX WITH A PYRIDYL INHIBITOR (COMPOUND 18)
 
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 :  1.75
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 (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

(-) Compounds

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

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): A  
Biological Unit 2 (1x):  B 
Biological Unit 3 (1x):   C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (7, 18)

Asymmetric Unit (7, 18)
No.NameCountTypeFull Name
131A3Ligand/IonN-[2-(3-METHOXYPHENYL)ETHANIMIDOYL]-2-PIPERIDIN-4-YLOXY-BENZAMIDE
2CL3Ligand/IonCHLORIDE ION
3DMS4Ligand/IonDIMETHYL SULFOXIDE
4GOA1Ligand/IonGLYCOLIC ACID
5MG3Ligand/IonMAGNESIUM ION
6NHW3Ligand/Ion2-OXOPENTADECYL-COA
7SO41Ligand/IonSULFATE ION
Biological Unit 1 (3, 4)
No.NameCountTypeFull Name
131A1Ligand/IonN-[2-(3-METHOXYPHENYL)ETHANIMIDOYL]-2-PIPERIDIN-4-YLOXY-BENZAMIDE
2CL-1Ligand/IonCHLORIDE ION
3DMS2Ligand/IonDIMETHYL SULFOXIDE
4GOA-1Ligand/IonGLYCOLIC ACID
5MG-1Ligand/IonMAGNESIUM ION
6NHW1Ligand/Ion2-OXOPENTADECYL-COA
7SO4-1Ligand/IonSULFATE ION
Biological Unit 2 (4, 4)
No.NameCountTypeFull Name
131A1Ligand/IonN-[2-(3-METHOXYPHENYL)ETHANIMIDOYL]-2-PIPERIDIN-4-YLOXY-BENZAMIDE
2CL-1Ligand/IonCHLORIDE ION
3DMS1Ligand/IonDIMETHYL SULFOXIDE
4GOA-1Ligand/IonGLYCOLIC ACID
5MG-1Ligand/IonMAGNESIUM ION
6NHW1Ligand/Ion2-OXOPENTADECYL-COA
7SO41Ligand/IonSULFATE ION
Biological Unit 3 (4, 4)
No.NameCountTypeFull Name
131A1Ligand/IonN-[2-(3-METHOXYPHENYL)ETHANIMIDOYL]-2-PIPERIDIN-4-YLOXY-BENZAMIDE
2CL-1Ligand/IonCHLORIDE ION
3DMS1Ligand/IonDIMETHYL SULFOXIDE
4GOA1Ligand/IonGLYCOLIC ACID
5MG-1Ligand/IonMAGNESIUM ION
6NHW1Ligand/Ion2-OXOPENTADECYL-COA
7SO4-1Ligand/IonSULFATE ION

(-) Sites  (18, 18)

Asymmetric Unit (18, 18)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETYR 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 , ASN A:187 , TRP A:192 , GLN A:193 , ALA A:194 , TYR A:196 , THR A:197 , LEU A:202 , TYR A:393 , MG A:1411 , HOH A:2001 , HOH A:2003 , HOH A:2216 , HOH A:2222 , HOH A:2421 , HOH A:2422 , HOH A:2423 , HOH A:2424 , HOH A:2425 , HOH A:2426BINDING SITE FOR RESIDUE NHW A1000
02AC2SOFTWAREVAL A:96 , GLU A:97 , ASP A:98 , PHE A:103 , PHE A:105 , TYR A:107 , THR A:197 , TYR A:211 , PHE A:226 , TYR A:315 , SER A:319 , TYR A:334 , LEU A:388 , LEU A:409 , LEU A:410 , HOH A:2235 , HOH A:2237 , HOH A:2368BINDING SITE FOR RESIDUE 31A A1001
03AC3SOFTWARELEU A:169 , SER A:171 , LYS A:172 , ARG A:173 , LEU A:174 , NHW A:1000BINDING SITE FOR RESIDUE MG A1411
04AC4SOFTWARELYS A:180 , THR A:247 , LEU A:248 , ARG A:358BINDING SITE FOR RESIDUE CL A1412
05AC5SOFTWAREGLU A:159 , PHE A:281 , TRP A:289 , HOH A:2373BINDING SITE FOR RESIDUE DMS A1413
06AC6SOFTWAREASN A:295 , SER A:316 , ASN A:359 , PHE A:361BINDING SITE FOR RESIDUE DMS A1414
07AC7SOFTWARETYR B:28 , LYS B:29 , PHE B:30 , TRP B:31 , ASN B:94 , TYR B:95 , VAL B:96 , VAL B:160 , 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 , TYR B:196 , THR B:197 , LEU B:202 , TYR B:393 , MG B:1412 , HOH B:2001 , HOH B:2003 , HOH B:2181 , HOH B:2184 , HOH B:2372 , HOH B:2373 , HOH B:2374 , HOH B:2375 , HOH B:2376 , HOH B:2377BINDING SITE FOR RESIDUE NHW B1000
08AC8SOFTWAREVAL B:96 , GLU B:97 , ASP B:98 , PHE B:103 , PHE B:105 , TYR B:107 , THR B:197 , TYR B:211 , TYR B:315 , SER B:319 , TYR B:334 , LEU B:409 , LEU B:410 , HOH B:2199 , HOH B:2201BINDING SITE FOR RESIDUE 31A B1001
09AC9SOFTWAREARG A:210 , LYS A:373 , ARG B:210 , LYS B:373 , HOH B:2212BINDING SITE FOR RESIDUE SO4 B1411
10BC1SOFTWARELEU B:169 , SER B:171 , LYS B:172 , ARG B:173 , LEU B:174 , NHW B:1000BINDING SITE FOR RESIDUE MG B1412
11BC2SOFTWARELYS B:180 , THR B:247 , LEU B:248 , ARG B:358 , HOH B:2264BINDING SITE FOR RESIDUE CL B1413
12BC3SOFTWAREGLU B:159 , PHE B:281 , TRP B:289 , HOH B:2333BINDING SITE FOR RESIDUE DMS B1414
13BC4SOFTWARETYR 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 , TRP C:192 , ALA C:194 , THR C:197 , LEU C:202 , TYR C:393 , MG C:1411 , HOH C:2001 , HOH C:2189 , HOH C:2196 , HOH C:2360 , HOH C:2361 , HOH C:2362 , HOH C:2363 , HOH C:2364BINDING SITE FOR RESIDUE NHW C1000
14BC5SOFTWAREVAL C:96 , GLU C:97 , ASP C:98 , PHE C:103 , PHE C:105 , TYR C:107 , THR C:197 , TYR C:211 , SER C:319 , TYR C:334 , LEU C:388 , LEU C:409 , LEU C:410 , HOH C:2209BINDING SITE FOR RESIDUE 31A C1001
15BC6SOFTWARELEU C:169 , SER C:171 , LYS C:172 , ARG C:173 , LEU C:174 , NHW C:1000BINDING SITE FOR RESIDUE MG C1411
16BC7SOFTWARELYS C:180 , LEU C:248 , ARG C:358BINDING SITE FOR RESIDUE CL C1412
17BC8SOFTWAREGLU C:159 , PHE C:281 , TRP C:289 , HOH C:2315BINDING SITE FOR RESIDUE DMS C1413
18BC9SOFTWAREALA C:115 , GLU C:159 , ASN C:161 , PHE C:162 , LEU C:410 , HOH C:2162BINDING SITE FOR RESIDUE GOA C1414

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4UFV)

(-) Sequences/Alignments

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.....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
                 4ufv 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....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
                 4ufv 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:372
                                                                                                                                                                                                                                                                                                                                                                                                                    
               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
                 4ufv C  26 MDYKFWYTQPVPKINDEFNESVNEPFISDNKVEDVRKDEYKLPPGYSWYVCDVKDEKDRSEIYTLLTDNYVEDDDNIFRFNYSAEFLLWALTSPNYLKTWHIGVKYDASNKLIGFISAIPTDICIHKRTIKMAEVNFLCVHKTLRSKRLAPVLIKEITRRINLENIWQAIYTAGVYLPKPVSDARYYHRSINVKKLIEIGFKLYRVEDTLNIKNMRLMKKKDVEGVHKLLGSYLEQFNLYAVFTKEEIAHWFLPIENVIYTYVNEENGKIKDMISFYSLPSQILGNDKYSTLNAAYSFYNVTTTATFKQLMQDAILLAKRNNFDVFNALEVMQNKSVFEDLKFGEGDGSLKYYLYNWKCASFAPAHVGIVLL 410
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225||     248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408  
                                                                                                                                                                                                                                  226|                                                                                                                                                                          
                                                                                                                                                                                                                                   240
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  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (4, 4)

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        A5K1A2_PLAVS | A5K1A2: 2ync 2ynd 2yne 4a95 4b10 4b11 4b12 4b13 4b14 4bbh 4c68 4cae 4caf 4ufw 4ufx 5g1z 5g22

(-) Related Entries Specified in the PDB File

4ufw PLASMODIUM VIVAX N-MYRISTOYLTRANSFERASE IN COMPLEX WITH A PYRIDYL INHIBITOR (COMPOUND 23)
4ufx PLASMODIUM VIVAX N-MYRISTOYLTRANSFERASE IN COMPLEX WITH A PYRIDYL INHIBITOR (COMPOUND 20)