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(-) Description

Title :  CRYSTAL STRUCTURE OF TERNARY COMPLEX OF PLASMODIUM VIVAX SHMT WITH GLYCINE AND A NOVEL PYRAZOLOPYRAN 99S: METHYL 5-{3-[(4S)-6-AMINO-5-CYANO-3-METHYL-4-(PROPAN-2-YL)-2,4-DIHYDROPYRANO[2,3-C]PYRAZOL-4-YL]-5-CYANOPHENYL}THIOPHENE-2-CARBOXYLATE .
 
Authors :  P. Chitnumsub, A. Jaruwat, U. Leartsakulpanich, M. C. Witschel
Date :  02 Jun 14  (Deposition) - 25 Mar 15  (Release) - 22 Apr 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C  (2x)
Keywords :  Alpha And Beta Protein, Transferase, Methyltransferase Activity, Inhibitor, Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. C. Witschel, M. Rottmann, A. Schwab, U. Leartsakulpanich, P. Chitnumsub, M. Seet, S. Tonazzi, G. Schwertz, F. Stelzer, T. Mietzner, C. Mcnamara, F. Thater, C. Freymond, A. Jaruwat, C. Pinthong, P. Riangrungroj, M. Oufir, M. Hamburger, P. Maser, L. M. Sanz-Alonso, S. Charman, S. Wittlin, Y. Yuthavong, P. Chaiyen, F. Diederich
Inhibitors Of Plasmodial Serine Hydroxymethyltransferase (Shmt): Cocrystal Structures Of Pyrazolopyrans With Potent Blood- And Liver-Stage Activities.
J. Med. Chem. V. 58 3117 2015
PubMed-ID: 25785478  |  Reference-DOI: 10.1021/JM501987H

(-) Compounds

Molecule 1 - SERINE HYDROXYMETHYLTRANSFERASE, PUTATIVE
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET17B
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: PVX_100730
    Organism Scientific: PLASMODIUM VIVAX
    Organism Taxid: 126793
    Other Details: PLASMODIUM VIVAX SHMT WITH PLP-GLYCINE SCHIFF BASE AND A NOVEL PYRAZOLOPYRAN 99S
    Strain: SALVADOR I

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): AB 
Biological Unit 2 (2x):   C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 8)

Asymmetric Unit (3, 8)
No.NameCountTypeFull Name
199S3Ligand/IonMETHYL 5-{3-[(4S)-6-AMINO-5-CYANO-3-METHYL-4-(PROPAN-2-YL)-2,4-DIHYDROPYRANO[2,3-C]PYRAZOL-4-YL]-5-CYANOPHENYL}THIOPHENE-2-CARBOXYLATE
2CL2Ligand/IonCHLORIDE ION
3PLG3Ligand/IonN-GLYCINE-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YL-METHANE]
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
199S2Ligand/IonMETHYL 5-{3-[(4S)-6-AMINO-5-CYANO-3-METHYL-4-(PROPAN-2-YL)-2,4-DIHYDROPYRANO[2,3-C]PYRAZOL-4-YL]-5-CYANOPHENYL}THIOPHENE-2-CARBOXYLATE
2CL-1Ligand/IonCHLORIDE ION
3PLG2Ligand/IonN-GLYCINE-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YL-METHANE]
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
199S2Ligand/IonMETHYL 5-{3-[(4S)-6-AMINO-5-CYANO-3-METHYL-4-(PROPAN-2-YL)-2,4-DIHYDROPYRANO[2,3-C]PYRAZOL-4-YL]-5-CYANOPHENYL}THIOPHENE-2-CARBOXYLATE
2CL-1Ligand/IonCHLORIDE ION
3PLG2Ligand/IonN-GLYCINE-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YL-METHANE]

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:34 , SER A:100 , GLY A:101 , SER A:102 , HIS A:129 , THR A:183 , ASP A:208 , HIS A:211 , THR A:234 , HIS A:236 , LYS A:237 , ARG A:371 , HOH A:654 , TYR B:54 , GLU B:56 , TYR B:64 , GLY B:271 , GLY B:272binding site for residue PLG A 501
2AC2SOFTWARELEU A:124 , GLY A:128 , HIS A:129 , LEU A:130 , VAL A:141 , THR A:183 , SER A:184 , ASN A:354 , LYS A:355 , ASN A:356 , THR A:357 , CYS A:364 , PRO A:367 , ARG A:371 , GLU B:56 , TYR B:63 , TYR B:64binding site for residue 99S A 502
3AC3SOFTWARETYR A:54 , GLU A:56 , TYR A:64 , GLY A:271 , GLY A:272 , HOH A:653 , SER B:34 , SER B:100 , GLY B:101 , SER B:102 , HIS B:129 , THR B:183 , ASP B:208 , HIS B:211 , THR B:234 , HIS B:236 , LYS B:237 , ARG B:371 , HOH B:642binding site for residue PLG B 501
4AC4SOFTWAREGLU A:56 , TYR A:63 , TYR A:64 , PRO A:267 , LEU B:124 , GLY B:128 , HIS B:129 , LEU B:130 , VAL B:141 , THR B:183 , SER B:184 , LYS B:355 , ASN B:356 , THR B:357 , CYS B:364 , PRO B:367 , ARG B:371binding site for residue 99S B 502
5AC5SOFTWAREASN A:276 , LYS A:277 , ASN B:276 , LYS B:277binding site for residue CL B 503
6AC6SOFTWARESER C:34 , TYR C:54 , GLU C:56 , TYR C:64 , SER C:100 , GLY C:101 , SER C:102 , HIS C:129 , TYR C:182 , THR C:183 , ASP C:208 , HIS C:211 , THR C:234 , HIS C:236 , LYS C:237 , GLY C:271 , GLY C:272 , ARG C:371 , HOH C:611binding site for residue PLG C 501
7AC7SOFTWAREGLU C:56 , TYR C:63 , TYR C:64 , LEU C:124 , GLY C:128 , HIS C:129 , LEU C:130 , VAL C:141 , THR C:183 , SER C:184 , ASN C:354 , LYS C:355 , ASN C:356 , THR C:357 , CYS C:364 , PRO C:367 , ARG C:371binding site for residue 99S C 502
8AC8SOFTWAREASN C:276 , LYS C:277binding site for residue CL C 503

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Phe A:266 -Pro A:267
2Phe B:266 -Pro B:267
3Phe C:266 -Pro C:267

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4TMR)

(-) 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:442
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhhhh.ee........hhhhhhhhhhhhhhh...ee..ee....hhhhhhhhhhhhhhhhhhh......eeee....hhhhhhhhhhhhhhh...eeeee.hhhh.hhhhh........hhhhh..eeeee........hhhhhhhhhhhhh..eeee.........hhhhhhhhhhhh..eeeee...hhhhhhh...........eeeee..........eeeeee.....hhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhh....eeeee.hhhh.hhhhhhhhhhhh.ee.eee............eeeeehhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhh...hhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4tmr A   1 MFNNEPLEQIDKELHDILADEEKRQRETINLIASENLTNGAVRECLGNRVSNKYSEGYPKKRYYGGNDFIDKIEELCQKRALEAFNVSDEEWGVNVQPLSGSAANVQALYALVGVKGKIMGMHLCSGGHLTHGFFDEKKKVSITSDMFESKLYKCNSQGYVDLDAVREMALSFKPKVIICGYTSYPRDIDYQQFRQICDEVNAYLFADISHISSFVACNILNNPFLHADVVTTTTHKILRGPRSALIFFNKKRNPGIEQKINSAVFPSFQGGPHNNKIAAVACQLKEVHSPAFKEYTQQVLLNSKALAKALISKQIDLVTNGTDNHLIVVDLRKFSITGSKLQETCNAINVSLNKNTIPSDVDCVSPSGVRIGTPAMTTRGAKEKDMEFIADVLARAIKITVDLQEQYGKKLVDFKKGLPGNAQLQQLKQEVVTWAGALPFP 442
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440  


Chain B from PDB  Type:PROTEIN  Length:442
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhhhh.ee..........hhhhhhhhhhhhh...ee..ee....hhhhhhhhhhhhhhhhhhh......eeee....hhhhhhhhhhhhhh....eeeee.hhhh..............hhhhhh.eeeee........hhhhhhhhhhhhh..eeee.........hhhhhhhhhhhh..eeeee...hhhhhhhh...hhhhh..eeeee..........eeeeee.....hhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhh....eeeee.hhhh.hhhhhhhhhhhh.ee.eee............eeeeehhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhh...hhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4tmr B   1 MFNNEPLEQIDKELHDILADEEKRQRETINLIASENLTNGAVRECLGNRVSNKYSEGYPKKRYYGGNDFIDKIEELCQKRALEAFNVSDEEWGVNVQPLSGSAANVQALYALVGVKGKIMGMHLCSGGHLTHGFFDEKKKVSITSDMFESKLYKCNSQGYVDLDAVREMALSFKPKVIICGYTSYPRDIDYQQFRQICDEVNAYLFADISHISSFVACNILNNPFLHADVVTTTTHKILRGPRSALIFFNKKRNPGIEQKINSAVFPSFQGGPHNNKIAAVACQLKEVHSPAFKEYTQQVLLNSKALAKALISKQIDLVTNGTDNHLIVVDLRKFSITGSKLQETCNAINVSLNKNTIPSDVDCVSPSGVRIGTPAMTTRGAKEKDMEFIADVLARAIKITVDLQEQYGKKLVDFKKGLPGNAQLQQLKQEVVTWAGALPFP 442
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440  


Chain C from PDB  Type:PROTEIN  Length:442
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhhhh.ee........hhhhhhhhhhhhhhh...ee..ee....hhhhhhhhhhhhhhhhhhh......eeee....hhhhhhhhhhhhhhh...eeeee.hhhh.hhhhh........hhhhh..eeeee........hhhhhhhhhhhhh..eeee.........hhhhhhhhhhh...eeeee...hhhhhhh....hhhhh..eeeee..........eeeeee......hhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..ee.hhh....eeeee.hhhh.hhhhhhhhhhhh.ee.eee............eeeeehhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhh...hhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4tmr C   1 MFNNEPLEQIDKELHDILADEEKRQRETINLIASENLTNGAVRECLGNRVSNKYSEGYPKKRYYGGNDFIDKIEELCQKRALEAFNVSDEEWGVNVQPLSGSAANVQALYALVGVKGKIMGMHLCSGGHLTHGFFDEKKKVSITSDMFESKLYKCNSQGYVDLDAVREMALSFKPKVIICGYTSYPRDIDYQQFRQICDEVNAYLFADISHISSFVACNILNNPFLHADVVTTTTHKILRGPRSALIFFNKKRNPGIEQKINSAVFPSFQGGPHNNKIAAVACQLKEVHSPAFKEYTQQVLLNSKALAKALISKQIDLVTNGTDNHLIVVDLRKFSITGSKLQETCNAINVSLNKNTIPSDVDCVSPSGVRIGTPAMTTRGAKEKDMEFIADVLARAIKITVDLQEQYGKKLVDFKKGLPGNAQLQQLKQEVVTWAGALPFP 442
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440
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  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 4TMR)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (4, 4)

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 Related Entries

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

UniProtKB/Swiss-Prot
        A5K8L9_PLAVS | A5K8L9: 5gvk 5gvl 5gvm 5gvn 5gvp
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        A5K8L9_PLAVS | A5K8L9: 4oyt 4pff 4pfn 4tn4

(-) Related Entries Specified in the PDB File

4o6z 4O6Z IS THE CRYSTAL STRUCTURE OF PLASMODIUM FALCIPARUM SHMT IN COMPLEX WITH PLP SCHIFF BASE.
4oyt 4OYT IS THE CRYSTAL STRUCTURE OF PLASMODIUM VIVAX SHMT IN COMPLEX WITH D-SERINE AND [6R]-5FTHF.
4pff 4PFF IS THE CRYSTAL STRUCTURE OF PLASMODIUM VIVAX SHMT IN COMPLEX WITH PLP SCHIFF BASE.
4pfn 4PFN IS THE CRYSTAL STRUCTURE OF PLASMODIUM VIVAX SHMT IN COMPLEX WITH L-SERINE.
4tn4 4O6Z IS THE CRYSTAL STRUCTURE OF PLASMODIUM FALCIPARUM SHMT IN COMPLEX WITH GLYCINE AND A NOVEL PYRAZOLOPYRAN 33G