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(-) Description

Title :  PLASMODIUM VIVAX N-MYRISTOYLTRANSFERASE IN COMPLEX WITH A QUINOLINE INHIBITOR (COMPOUND 1)
 
Authors :  V. Goncalves, J. A. Brannigan, A. Laporte, A. S. Bell, S. M. Roberts, A. J. Wilkinson, R. J. Leatherbarrow, E. W. Tate
Date :  06 Apr 16  (Deposition) - 15 Feb 17  (Release) - 28 Jun 17  (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, Quinoline, Drug Design (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. Goncalves, J. A. Brannigan, A. Laporte, A. S. Bell, S. M. Roberts, A. J. Wilkinson, R. J. Leatherbarrow, E. W. Tate
Structure-Guided Optimization Of Quinoline Inhibitors Of Plasmodium N-Myristoyltransferase.
Medchemcomm V. 8 191 2017
PubMed-ID: 28626547  |  Reference-DOI: 10.1039/C6MD00531D

(-) 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
    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, 18)

Asymmetric Unit (6, 18)
No.NameCountTypeFull Name
1CL3Ligand/IonCHLORIDE ION
2DMS4Ligand/IonDIMETHYL SULFOXIDE
3MG3Ligand/IonMAGNESIUM ION
4NHW3Ligand/Ion2-OXOPENTADECYL-COA
5SO42Ligand/IonSULFATE ION
6U533Ligand/IonETHYL 4-(2-CYANOETHYLSULFANYL)-6-METHOXY-QUINOLINE-3-CARBOXYLATE
Biological Unit 1 (4, 5)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2DMS1Ligand/IonDIMETHYL SULFOXIDE
3MG-1Ligand/IonMAGNESIUM ION
4NHW1Ligand/Ion2-OXOPENTADECYL-COA
5SO42Ligand/IonSULFATE ION
6U531Ligand/IonETHYL 4-(2-CYANOETHYLSULFANYL)-6-METHOXY-QUINOLINE-3-CARBOXYLATE
Biological Unit 2 (3, 3)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2DMS1Ligand/IonDIMETHYL SULFOXIDE
3MG-1Ligand/IonMAGNESIUM ION
4NHW1Ligand/Ion2-OXOPENTADECYL-COA
5SO4-1Ligand/IonSULFATE ION
6U531Ligand/IonETHYL 4-(2-CYANOETHYLSULFANYL)-6-METHOXY-QUINOLINE-3-CARBOXYLATE
Biological Unit 3 (3, 4)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2DMS2Ligand/IonDIMETHYL SULFOXIDE
3MG-1Ligand/IonMAGNESIUM ION
4NHW1Ligand/Ion2-OXOPENTADECYL-COA
5SO4-1Ligand/IonSULFATE ION
6U531Ligand/IonETHYL 4-(2-CYANOETHYLSULFANYL)-6-METHOXY-QUINOLINE-3-CARBOXYLATE

(-) 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 , 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:2341 , HOH A:2350 , HOH A:2608 , HOH A:2609 , HOH A:2610 , HOH A:2611 , HOH A:2612 , HOH A:2613BINDING SITE FOR RESIDUE NHW A 1000
02AC2SOFTWAREVAL A:96 , GLU A:97 , ASP A:98 , PHE A:103 , PHE A:105 , TYR A:211 , HIS A:213 , PHE A:226 , SER A:319 , TYR A:334 , ASN A:365 , HOH A:2542 , HOH A:2593BINDING SITE FOR RESIDUE U53 A 1001
03AC3SOFTWARETYR 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 , 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:2266 , HOH B:2272 , HOH B:2273 , HOH B:2500 , HOH B:2501 , HOH B:2502 , HOH B:2503 , HOH B:2504 , HOH B:2505BINDING SITE FOR RESIDUE NHW B 1000
04AC4SOFTWAREVAL B:96 , GLU B:97 , ASP B:98 , PHE B:103 , PHE B:105 , TYR B:211 , HIS B:213 , PHE B:226 , SER B:319 , TYR B:334 , ASN B:365 , HOH B:2440BINDING SITE FOR RESIDUE U53 B 1001
05AC5SOFTWARETYR 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 , ALA C:194 , TYR C:196 , THR C:197 , LEU C:202 , TYR C:393 , MG C:1413 , HOH C:2001 , HOH C:2002 , HOH C:2269 , HOH C:2275 , HOH C:2276 , HOH C:2501 , HOH C:2502 , HOH C:2503 , HOH C:2504 , HOH C:2505 , HOH C:2506BINDING SITE FOR RESIDUE NHW C 1000
06AC6SOFTWAREVAL C:96 , GLU C:97 , ASP C:98 , PHE C:103 , PHE C:105 , PHE C:226 , SER C:319 , LEU C:330 , ALA C:332 , TYR C:334 , VAL C:363 , ASN C:365 , DMS C:1411 , HOH C:2428 , HOH C:2468BINDING SITE FOR RESIDUE U53 C 1001
07AC7SOFTWARETYR C:315 , TYR C:334 , LEU C:410 , U53 C:1001 , HOH C:2309 , HOH C:2508BINDING SITE FOR RESIDUE DMS C 1411
08AC8SOFTWAREGLU A:159 , PHE A:281 , TRP A:289 , HOH A:2547BINDING SITE FOR RESIDUE DMS A 1411
09AC9SOFTWAREGLU B:159 , PHE B:281 , TRP B:289 , HOH B:2445BINDING SITE FOR RESIDUE DMS B 1411
10BC1SOFTWAREGLU C:159 , PHE C:281 , TRP C:289 , HOH C:2442BINDING SITE FOR RESIDUE DMS C 1412
11BC2SOFTWARELEU A:169 , SER A:171 , LYS A:172 , ARG A:173 , LEU A:174 , NHW A:1000BINDING SITE FOR RESIDUE MG A 1412
12BC3SOFTWARELEU B:169 , SER B:171 , LYS B:172 , ARG B:173 , LEU B:174 , NHW B:1000BINDING SITE FOR RESIDUE MG B 1412
13BC4SOFTWARELEU C:169 , SER C:171 , LYS C:172 , ARG C:173 , LEU C:174 , NHW C:1000BINDING SITE FOR RESIDUE MG C 1413
14BC5SOFTWAREARG A:210 , TYR A:212 , LYS A:373 , HOH A:2383 , HOH A:2614 , HOH A:2615 , ARG B:210 , TYR B:212 , LYS B:373BINDING SITE FOR RESIDUE SO4 A 1413
15BC6SOFTWAREASN A:295 , TYR A:298 , SER A:316 , ASN A:359 , PHE A:361 , HOH A:2538BINDING SITE FOR RESIDUE SO4 A 1414
16BC7SOFTWARELYS A:180 , THR A:247 , LEU A:248 , ARG A:358 , HOH A:2107BINDING SITE FOR RESIDUE CL A 1415
17BC8SOFTWARELYS B:180 , THR B:247 , LEU B:248 , ARG B:358BINDING SITE FOR RESIDUE CL B 1413
18BC9SOFTWARELYS C:180 , THR C:247 , LEU C:248 , ARG C:358BINDING SITE FOR RESIDUE CL C 1414

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5G1Z)

(-) 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 5G1Z)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5G1Z)

(-) Exons   (0, 0)

(no "Exon" information available for 5G1Z)

(-) 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..hhhhhhhhhhhhhhhhh...eeeeee........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
                 5g1z A  26 IDYKFWYTQPVPKINDEFNESVNEPFISDNKVEDVRKDEYKLPPGYSWYVCDVKDEKDRSEIYTLLTDNYVEDDDNIFRFNYSAEFLLWALTSPNYLKTWHIGVKYDASNKLIGFISAIPTDICIHKRTIKMAEVNFLCVHKTLRSKRLAPVLIKEITRRINLENIWQAIYTAGVYLPKPVSDARYYHRSINVKKLIEIGFSSLNSRLTMSRAIKLYRVEDTLNIKNMRLMKKKDVEGVHKLLGSYLEQFNLYAVFTKEEIAHWFLPIENVIYTYVNEENGKIKDMISFYSLPSQILGNDKYSTLNAAYSFYNVTTTATFKQLMQDAILLAKRNNFDVFNALEVMQNKSVFEDLKFGEGDGSLKYYLYNWKCASFAPAHVGIVLL 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.........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
                 5g1z B  26 IDYKFWYTQPVPKINDEFNESVNEPFISDNKVEDVRKDEYKLPPGYSWYVCDVKDEKDRSEIYTLLTDNYVEDDDNIFRFNYSAEFLLWALTSPNYLKTWHIGVKYDASNKLIGFISAIPTDICIHKRTIKMAEVNFLCVHKTLRSKRLAPVLIKEITRRINLENIWQAIYTAGVYLPKPVSDARYYHRSINVKKLIEIGFSSLNSRLTMSRAIKLYRVEDTLNIKNMRLMKKKDVEGVHKLLGSYLEQFNLYAVFTKEEIAHWFLPIENVIYTYVNEENGKIKDMISFYSLPSQILGNDKYSTLNAAYSFYNVTTTATFKQLMQDAILLAKRNNFDVFNALEVMQNKSVFEDLKFGEGDGSLKYYLYNWKCASFAPAHVGIVLL 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:370
                                                                                                                                                                                                                                                                                                                                                                                                                  
               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........eee.eeeee.hhhhhhhhh..............ee.hhhhhhhhhhhhhhhhh...eee..hhhhhhhhhh.....eeeeeeee..eeeeeeeeee..eee.......ee.eeee...ee...hhhhhhhhhhhhhhhh...eeeee...hhhhhh.....ee....eeeeee..ee...hhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5g1z C  27 DYKFWYTQPVPKINDEFNESVNEPFISDNKVEDVRKDEYKLPPGYSWYVCDVKDEKDRSEIYTLLTDNYVEDDDNIFRFNYSAEFLLWALTSPNYLKTWHIGVKYDASNKLIGFISAIPTDICIHKRTIKMAEVNFLCVHKTLRSKRLAPVLIKEITRRINLENIWQAIYTAGVYLPKPVSDARYYHRSINVKKLIEIGFLYRVEDTLNIKNMRLMKKKDVEGVHKLLGSYLEQFNLYAVFTKEEIAHWFLPIENVIYTYVNEENGKIKDMISFYSLPSQILGNDKYSTLNAAYSFYNVTTTATFKQLMQDAILLAKRNNFDVFNALEVMQNKSVFEDLKFGEGDGSLKYYLYNWKCASFAPAHVGIVLL 410
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226|      250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410
                                                                                                                                                                                                                                 226|                                                                                                                                                                         
                                                                                                                                                                                                                                  241
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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 5G1Z)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5G1Z)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5G1Z)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

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

(-) Related Entries Specified in the PDB File

5g20 LEISHMANIA MAJOR N-MYRISTOYLTRANSFERASE IN COMPLEX WITH A QUINOLINE INHIBITOR (COMPOUND 19).
5g21 LEISHMANIA MAJOR N-MYRISTOYLTRANSFERASE IN COMPLEX WITH A QUINOLINE INHIBITOR (COMPOUND 26).
5g22 PLASMODIUM VIVAX N-MYRISTOYLTRANSFERASE IN COMPLEX WITH A QUINOLINE INHIBITOR (COMPOUND 26)