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(-) Description

Title :  PLASMODIUM VIVAX N-MYRISTOYLTRANSFERASE IN COMPLEX WITH A PYRIDYL INHIBITOR (COMPOUND 19)
 
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 :  1.49
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

(-) 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
    Expression System Vector Type: PLASMID
    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  (6, 22)

Asymmetric Unit (6, 22)
No.NameCountTypeFull Name
180O3Ligand/IonN-[2-(3-METHOXYPHENYL)ETHANIMIDOYL]-2-PIPERIDIN-4-YLOXY-PYRIDINE-3-CARBOXAMIDE
2CL6Ligand/IonCHLORIDE ION
3DMS5Ligand/IonDIMETHYL SULFOXIDE
4MG3Ligand/IonMAGNESIUM ION
5NHW3Ligand/Ion2-OXOPENTADECYL-COA
6SO42Ligand/IonSULFATE ION
Biological Unit 1 (4, 5)
No.NameCountTypeFull Name
180O1Ligand/IonN-[2-(3-METHOXYPHENYL)ETHANIMIDOYL]-2-PIPERIDIN-4-YLOXY-PYRIDINE-3-CARBOXAMIDE
2CL-1Ligand/IonCHLORIDE ION
3DMS2Ligand/IonDIMETHYL SULFOXIDE
4MG-1Ligand/IonMAGNESIUM ION
5NHW1Ligand/Ion2-OXOPENTADECYL-COA
6SO41Ligand/IonSULFATE ION
Biological Unit 2 (4, 5)
No.NameCountTypeFull Name
180O1Ligand/IonN-[2-(3-METHOXYPHENYL)ETHANIMIDOYL]-2-PIPERIDIN-4-YLOXY-PYRIDINE-3-CARBOXAMIDE
2CL-1Ligand/IonCHLORIDE ION
3DMS2Ligand/IonDIMETHYL SULFOXIDE
4MG-1Ligand/IonMAGNESIUM ION
5NHW1Ligand/Ion2-OXOPENTADECYL-COA
6SO41Ligand/IonSULFATE ION
Biological Unit 3 (3, 3)
No.NameCountTypeFull Name
180O1Ligand/IonN-[2-(3-METHOXYPHENYL)ETHANIMIDOYL]-2-PIPERIDIN-4-YLOXY-PYRIDINE-3-CARBOXAMIDE
2CL-1Ligand/IonCHLORIDE ION
3DMS1Ligand/IonDIMETHYL SULFOXIDE
4MG-1Ligand/IonMAGNESIUM ION
5NHW1Ligand/Ion2-OXOPENTADECYL-COA
6SO4-1Ligand/IonSULFATE ION

(-) Sites  (22, 22)

Asymmetric Unit (22, 22)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREVAL A:96 , GLU A:97 , ASP A:98 , PHE A:103 , PHE A:105 , TYR A:107 , THR A:197 , TYR A:211 , TYR A:315 , LEU A:317 , SER A:319 , TYR A:334 , LEU A:367 , LEU A:388 , LEU A:409 , LEU A:410 , HOH A:2345 , HOH A:2346 , HOH A:2494 , HOH A:2506BINDING SITE FOR RESIDUE 80O A1000
02AC2SOFTWARETYR 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:1412 , HOH A:2001 , HOH A:2004 , HOH A:2319 , HOH A:2327 , HOH A:2576 , HOH A:2577 , HOH A:2578 , HOH A:2579 , HOH A:2580 , HOH A:2581 , HOH A:2582BINDING SITE FOR RESIDUE NHW A1001
03AC3SOFTWAREARG A:210 , HOH A:2537 , HOH A:2583 , ARG B:210 , LYS B:373BINDING SITE FOR RESIDUE SO4 A1411
04AC4SOFTWARELEU A:169 , SER A:171 , LYS A:172 , ARG A:173 , LEU A:174 , NHW A:1001BINDING SITE FOR RESIDUE MG A1412
05AC5SOFTWARELYS A:180 , THR A:247 , LEU A:248 , ARG A:358BINDING SITE FOR RESIDUE CL A1413
06AC6SOFTWAREALA A:401 , HOH B:2435BINDING SITE FOR RESIDUE CL A1414
07AC7SOFTWAREILE A:222 , GLY A:225 , SER A:227 , LYS B:62BINDING SITE FOR RESIDUE CL A1415
08AC8SOFTWAREGLU A:159 , PHE A:281 , TRP A:289 , LEU A:409 , HOH A:2509BINDING SITE FOR RESIDUE DMS A1416
09AC9SOFTWAREASN A:295 , ASN A:331 , ASN A:359 , ASN A:360 , PHE A:361BINDING SITE FOR RESIDUE DMS A1417
10BC1SOFTWAREVAL 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 , LEU B:317 , SER B:319 , TYR B:334 , LEU B:367 , LEU B:388 , LEU B:409 , LEU B:410 , HOH B:2256 , HOH B:2258 , HOH B:2397 , HOH B:2408BINDING SITE FOR RESIDUE 80O B1000
11BC2SOFTWARETYR 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 , 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:2005 , HOH B:2235 , HOH B:2240 , HOH B:2460 , HOH B:2461 , HOH B:2462 , HOH B:2463 , HOH B:2464 , HOH B:2465BINDING SITE FOR RESIDUE NHW B1001
12BC3SOFTWAREARG A:210 , LYS A:373 , HOH A:2359 , ARG B:210 , HOH B:2432BINDING SITE FOR RESIDUE SO4 B1411
13BC4SOFTWARELEU B:169 , SER B:171 , LYS B:172 , ARG B:173 , LEU B:174 , NHW B:1001BINDING SITE FOR RESIDUE MG B1412
14BC5SOFTWARELYS B:180 , THR B:247 , LEU B:248 , ARG B:358BINDING SITE FOR RESIDUE CL B1413
15BC6SOFTWAREALA B:401BINDING SITE FOR RESIDUE CL B1414
16BC7SOFTWAREGLU B:159 , PHE B:281 , TRP B:289 , LEU B:409 , HOH B:2411BINDING SITE FOR RESIDUE DMS B1415
17BC8SOFTWAREASN B:295 , SER B:316 , ASN B:359 , ASN B:360 , PHE B:361BINDING SITE FOR RESIDUE DMS B1416
18BC9SOFTWAREVAL C:96 , GLU C:97 , ASP C:98 , PHE C:103 , PHE C:105 , TYR C:107 , THR C:197 , TYR C:211 , TYR C:315 , LEU C:317 , SER C:319 , TYR C:334 , LEU C:367 , LEU C:409 , LEU C:410 , HOH C:2307 , HOH C:2309 , HOH C:2440BINDING SITE FOR RESIDUE 80O C1000
19CC1SOFTWARETYR 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 , TYR C:196 , THR C:197 , LEU C:202 , TYR C:393 , MG C:1411 , HOH C:2002 , HOH C:2003 , HOH C:2289 , HOH C:2294 , HOH C:2295 , HOH C:2513 , HOH C:2514 , HOH C:2515 , HOH C:2516 , HOH C:2517 , HOH C:2518BINDING SITE FOR RESIDUE NHW C1001
20CC2SOFTWARELEU C:169 , SER C:171 , LYS C:172 , ARG C:173 , LEU C:174 , NHW C:1001BINDING SITE FOR RESIDUE MG C1411
21CC3SOFTWARELYS C:180 , THR C:247 , LEU C:248 , ARG C:358 , HOH C:2094BINDING SITE FOR RESIDUE CL C1412
22CC4SOFTWAREGLU C:159 , PHE C:281 , TRP C:289 , HOH C:2454BINDING SITE FOR RESIDUE DMS C1413

(-) SS Bonds  (0, 0)

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

(-) 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 4UFX)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4UFX)

(-) 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.........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
                 4ufx 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.........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
                 4ufx 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
                 4ufx 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 4UFX)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (4, 4)

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  A5K1A2_PLAVS | A5K1A2
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

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

(-) Related Entries Specified in the PDB File

4ufv PLASMODIUM VIVAX N-MYRISTOYLTRANSFERASE IN COMPLEX WITH A PYRIDYL INHIBITOR (COMPOUND 19)
4ufw PLASMODIUM VIVAX N-MYRISTOYLTRANSFERASE IN COMPLEX WITH A PYRIDYL INHIBITOR (COMPOUND 23)