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(-) Description

Title :  CRYSTAL STRUCTURE OF PHOSPHOGLYCERATE KINASE FROM PLASMODIUM FALCIPARUM, IN THE OPEN CONFORMATION
 
Authors :  D. Chattopadhyay, B. Pal, C. D. Smith
Date :  20 May 02  (Deposition) - 29 Jul 03  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Keywords :  Pgk, Phosphoglycerate Kinase, Glycolysis, Glycerol, Open Conformation, Adp Complex, Selenomethionine, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  D. Chattopadhyay, B. Pal, C. D. Smith
Crystal Structure Of Phosphoglycerate Kinase From Plasmodiu Falciparum
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PHOSPHOGLYCERATE KINASE
    ChainsA, B, C
    EC Number2.7.2.3
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET15B
    Expression System StrainBL21(DE3)PLYSS
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GenePGK
    Organism CommonMALARIA PARASITE P. FALCIPARUM
    Organism ScientificPLASMODIUM FALCIPARUM
    Organism Taxid5833

 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  (4, 32)

Asymmetric Unit (4, 32)
No.NameCountTypeFull Name
1AMP3Ligand/IonADENOSINE MONOPHOSPHATE
2GOL1Ligand/IonGLYCEROL
3MSE25Mod. Amino AcidSELENOMETHIONINE
4SO43Ligand/IonSULFATE ION
Biological Unit 1 (4, 11)
No.NameCountTypeFull Name
1AMP1Ligand/IonADENOSINE MONOPHOSPHATE
2GOL1Ligand/IonGLYCEROL
3MSE8Mod. Amino AcidSELENOMETHIONINE
4SO41Ligand/IonSULFATE ION
Biological Unit 2 (3, 10)
No.NameCountTypeFull Name
1AMP1Ligand/IonADENOSINE MONOPHOSPHATE
2GOL-1Ligand/IonGLYCEROL
3MSE8Mod. Amino AcidSELENOMETHIONINE
4SO41Ligand/IonSULFATE ION
Biological Unit 3 (3, 11)
No.NameCountTypeFull Name
1AMP1Ligand/IonADENOSINE MONOPHOSPHATE
2GOL-1Ligand/IonGLYCEROL
3MSE9Mod. Amino AcidSELENOMETHIONINE
4SO41Ligand/IonSULFATE ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN C:26 , ARG C:66 , ARG C:122 , LYS C:138 , ARG C:170BINDING SITE FOR RESIDUE SO4 C 604
2AC2SOFTWAREHIS A:63 , ARG A:66 , ARG A:122 , ARG A:170BINDING SITE FOR RESIDUE SO4 A 605
3AC3SOFTWAREASN B:26 , HIS B:63 , ARG B:66 , ARG B:122 , ARG B:170BINDING SITE FOR RESIDUE SO4 B 606
4AC4SOFTWAREGLY A:213 , ALA A:214 , LYS A:215 , GLY A:237 , GLY A:238 , LEU A:256 , GLY A:340 , VAL A:341 , GLU A:343 , ASP A:374 , LYS B:140 , LYS B:143BINDING SITE FOR RESIDUE AMP A 501
5AC5SOFTWARELYS A:143 , GLY B:213 , ALA B:214 , LYS B:215 , LYS B:219 , GLY B:237 , GLY B:238 , LEU B:313 , GLY B:340 , VAL B:341 , GLU B:343 , ASP B:374BINDING SITE FOR RESIDUE AMP B 502
6AC6SOFTWARELYS C:140 , LYS C:143 , GLY C:213 , ALA C:214 , LYS C:215 , GLY C:237 , GLY C:238 , LEU C:256 , GLY C:340 , GLU C:343 , ASP C:374BINDING SITE FOR RESIDUE AMP C 503
7AC7SOFTWAREASN A:72 , LYS A:74 , TYR A:75 , LYS B:74BINDING SITE FOR RESIDUE GOL A 614

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1LTK)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Arg A:205 -Pro A:206
2Arg B:205 -Pro B:206
3Arg C:205 -Pro C:206

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1LTK)

(-) PROSITE Motifs  (1, 3)

Asymmetric Unit (1, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PGLYCERATE_KINASEPS00111 Phosphoglycerate kinase signature.PGK_PLAF718-28
 
 
  3A:18-28
B:18-28
C:18-28
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PGLYCERATE_KINASEPS00111 Phosphoglycerate kinase signature.PGK_PLAF718-28
 
 
  1A:18-28
-
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PGLYCERATE_KINASEPS00111 Phosphoglycerate kinase signature.PGK_PLAF718-28
 
 
  1-
B:18-28
-
Biological Unit 3 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PGLYCERATE_KINASEPS00111 Phosphoglycerate kinase signature.PGK_PLAF718-28
 
 
  1-
-
C:18-28

(-) Exons   (0, 0)

(no "Exon" information available for 1LTK)

(-) 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:417
 aligned with PGK_PLAF7 | P27362 from UniProtKB/Swiss-Prot  Length:416

    Alignment length:417
                              1                                                                                                                                                                                                                                                                                                                                                                                                                              
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       
            PGK_PLAF7     - --MLGNKLSISDLKDIKNKKVLVRVDFNVPIENGIIKDTNRITATLPTINHLKKEGASKIILISHCGRPDGLRNEKYTLKPVAETLKGLLGEEVLFLNDCVGKEVEDKINAAKENSVILLENLRFHIEEEGKGVDANGNKVKANKEDVEKFQNDLTKLADVFINDAFGTAHRAHSSMVGVKLNVKASGFLMKKELEYFSKALENPQRPLLAILGGAKVSDKIQLIKNLLDKVDRMIIGGGMAYTFKKVLNNMKIGTSLFDEAGSKIVGEIMEKAKAKNVQIFLPVDFKIADNFDNNANTKFVTDEEGIPDNWMGLDAGPKSIENYKDVILTSKTVIWNGPQGVFEMPNFAKGSIECLNLVVEVTKKGAITIVGGGDTASLVEQQNKKNEISHVSTGGGASLELLEGKELPGVLALSN 415
               SCOP domains d1ltka_ A: Phosphoglycerate kinase                                                                                                                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains ----1ltkA01 A:3-188  [code=3.40.50.1260, no name defined]                                                                                                                                     ------1ltkA02 A:195-403  [code=3.40.50.1270, no name defined]                                                                                                                                                          ------------ CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...................eeeeee.....ee..ee..hhhhhhhhhhhhhhhh....eeeee..........hhhhhhhhhhhhhhhhhh...ee.....hhhhhhhhhh....eeee..hhhhhhhhhheee.....eee.hhhhhhhhhhhhhh...eeeee........hhhhhh....eeeehhhhhhhhhhhhhhhh.....eeeeee...hhhhhhhhhhhhh...eeeee.hhhhhhhhhhhh..........hhhhhhhhhhhhhhhh..eee...eeeee........eeeee.........eeeeehhhhhhhhhhhhhh..eeeee.......hhhhhhhhhhhhhhhhhhhhh..eeee....hhhhhhhhhhhhhh.ee...hhhhhhhhh...hhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------PGLYCERATE_--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ltk A  -1 HHHLGNKLSISDLKDIKNKKVLVRVDFNVPIENGIIKDTNRITATLPTINHLKKEGASKIILISHCGRPDGLRNEKYTLKPVAETLKGLLGEEVLFLNDCVGKEVEDKINAAKENSVILLENLRFHIEEEGKGVDANGNKVKANKEDVEKFQNDLTKLADVFINDAFGTAHRAHSSmVGVKLNVKASGFLmKKELEYFSKALENPQRPLLAILGGAKVSDKIQLIKNLLDKVDRmIIGGGmAYTFKKVLNNmKIGTSLFDEAGSKIVGEImEKAKAKNVQIFLPVDFKIADNFDNNANTKFVTDEEGIPDNWmGLDAGPKSIENYKDVILTSKTVIWNGPQGVFEmPNFAKGSIECLNLVVEVTKKGAITIVGGGDTASLVEQQNKKNEISHVSTGGGASLELLEGKELPGVLALSN 415
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168      |178       188|      198       208       218       228    |  238|      248 |     258       268|      278       288       298       308  |    318       328       338     | 348       358       368       378       388       398       408       
                                                                                                                                                                                                          175-MSE       189-MSE                                     233-MSE |        250-MSE            269-MSE                                   311-MSE                          344-MSE                                                                   
                                                                                                                                                                                                                                                                          239-MSE                                                                                                                                                                            

Chain B from PDB  Type:PROTEIN  Length:415
 aligned with PGK_PLAF7 | P27362 from UniProtKB/Swiss-Prot  Length:416

    Alignment length:415
                                    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     
            PGK_PLAF7     1 MLGNKLSISDLKDIKNKKVLVRVDFNVPIENGIIKDTNRITATLPTINHLKKEGASKIILISHCGRPDGLRNEKYTLKPVAETLKGLLGEEVLFLNDCVGKEVEDKINAAKENSVILLENLRFHIEEEGKGVDANGNKVKANKEDVEKFQNDLTKLADVFINDAFGTAHRAHSSMVGVKLNVKASGFLMKKELEYFSKALENPQRPLLAILGGAKVSDKIQLIKNLLDKVDRMIIGGGMAYTFKKVLNNMKIGTSLFDEAGSKIVGEIMEKAKAKNVQIFLPVDFKIADNFDNNANTKFVTDEEGIPDNWMGLDAGPKSIENYKDVILTSKTVIWNGPQGVFEMPNFAKGSIECLNLVVEVTKKGAITIVGGGDTASLVEQQNKKNEISHVSTGGGASLELLEGKELPGVLALSN 415
               SCOP domains d1ltkb_ B: Phosphoglycerate kinase                                                                                                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains --1ltkB01 B:3-188  [code=3.40.50.1260, no name defined]                                                                                                                                     ------1ltkB02 B:195-403  [code=3.40.50.1270, no name defined]                                                                                                                                                          ------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................eeeeee...................hhhhhhhhhh....eeeee..........hhhhhhhhhhhhhhhhhh..eeee......hhhhhhh.....eeeee.hhhhh.....eee.....eee.hhhhhhhhhhhhhhh..eeeeehhhhh...hhhhhh.....eeehhhhhhhhhhhhhhhh.....eeeeee......hhhhhhhhhhhh.eeeee.hhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhh.......eeeee........eeeee.........eeeeehhhhhhhhhhhhhh..eee.........hhhhhhhhhhhhhhhhhhhhh..eeee...hhhhhhhhh.hhhhh.ee..hhhhhhhhhhh..hhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------PGLYCERATE_--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ltk B   1 HLGNKLSISDLKDIKNKKVLVRVDFNVPIENGIIKDTNRITATLPTINHLKKEGASKIILISHCGRPDGLRNEKYTLKPVAETLKGLLGEEVLFLNDCVGKEVEDKINAAKENSVILLENLRFHIEEEGKGVDANGNKVKANKEDVEKFQNDLTKLADVFINDAFGTAHRAHSSmVGVKLNVKASGFLmKKELEYFSKALENPQRPLLAILGGAKVSDKIQLIKNLLDKVDRmIIGGGmAYTFKKVLNNmKIGTSLFDEAGSKIVGEImEKAKAKNVQIFLPVDFKIADNFDNNANTKFVTDEEGIPDNWmGLDAGPKSIENYKDVILTSKTVIWNGPQGVFEmPNFAKGSIECLNLVVEVTKKGAITIVGGGDTASLVEQQNKKNEISHVSTGGGASLELLEGKELPGVLALSN 415
                                    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     
                                                                                                                                                                                                        175-MSE       189-MSE                                     233-MSE |        250-MSE            269-MSE                                   311-MSE                          344-MSE                                                                   
                                                                                                                                                                                                                                                                        239-MSE                                                                                                                                                                            

Chain C from PDB  Type:PROTEIN  Length:424
 aligned with PGK_PLAF7 | P27362 from UniProtKB/Swiss-Prot  Length:416

    Alignment length:424
                                    1                                                                                                                                                                                                                                                                                                                                                                                                                               
                                    |2        12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412    
            PGK_PLAF7     - --------MLGNKLSISDLKDIKNKKVLVRVDFNVPIENGIIKDTNRITATLPTINHLKKEGASKIILISHCGRPDGLRNEKYTLKPVAETLKGLLGEEVLFLNDCVGKEVEDKINAAKENSVILLENLRFHIEEEGKGVDANGNKVKANKEDVEKFQNDLTKLADVFINDAFGTAHRAHSSMVGVKLNVKASGFLMKKELEYFSKALENPQRPLLAILGGAKVSDKIQLIKNLLDKVDRMIIGGGMAYTFKKVLNNMKIGTSLFDEAGSKIVGEIMEKAKAKNVQIFLPVDFKIADNFDNNANTKFVTDEEGIPDNWMGLDAGPKSIENYKDVILTSKTVIWNGPQGVFEMPNFAKGSIECLNLVVEVTKKGAITIVGGGDTASLVEQQNKKNEISHVSTGGGASLELLEGKELPGVLALSNK 416
               SCOP domains d1ltkc_ C: Phosphoglycerate kinase                                                                                                                                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains ----------1ltkC01 C:3-188  [code=3.40.50.1260, no name defined]                                                                                                                                     ------1ltkC02 C:195-403  [code=3.40.50.1270, no name defined]                                                                                                                                                          ------------- CATH domains
           Pfam domains (1) --------------PGK-1ltkC01 C:7-405                                                                                                                                                                                                                                                                                                                                                                                            ----------- Pfam domains (1)
           Pfam domains (2) --------------PGK-1ltkC02 C:7-405                                                                                                                                                                                                                                                                                                                                                                                            ----------- Pfam domains (2)
           Pfam domains (3) --------------PGK-1ltkC03 C:7-405                                                                                                                                                                                                                                                                                                                                                                                            ----------- Pfam domains (3)
         Sec.struct. author .........................eeeee......ee..ee..hhhhhhhhhhhhhhhhh...eeeee..........hhhhhhhhhhhhhhhhhh...eee....hhhhhhhhhhh....eeee.hhhhh.....eee.....eee.hhhhhhhhhhhhhh...eeee.hhhhh...hhhhhh....eeeehhhhhhhhhhhhhhhh.....eeeee....hhhhhhhhhhhhh...eeee..hhhhhhhhhh..........hhhhhhhhhhhhhhhhhhh.eee...eeeee........eeeee.........eeeeehhhhhhhhhhhhhh..eeeee.......hhhhhhhhhhhhhhhhhhhhh..eeee.hhhhhhhhhhh.hhhhh.ee...hhhhhhhhh...hhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------PGLYCERATE_---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ltk C  -7 HSmHHHHHHLGNKLSISDLKDIKNKKVLVRVDFNVPIENGIIKDTNRITATLPTINHLKKEGASKIILISHCGRPDGLRNEKYTLKPVAETLKGLLGEEVLFLNDCVGKEVEDKINAAKENSVILLENLRFHIEEEGKGVDANGNKVKANKEDVEKFQNDLTKLADVFINDAFGTAHRAHSSmVGVKLNVKASGFLmKKELEYFSKALENPQRPLLAILGGAKVSDKIQLIKNLLDKVDRmIIGGGmAYTFKKVLNNmKIGTSLFDEAGSKIVGEImEKAKAKNVQIFLPVDFKIADNFDNNANTKFVTDEEGIPDNWmGLDAGPKSIENYKDVILTSKTVIWNGPQGVFEmPNFAKGSIECLNLVVEVTKKGAITIVGGGDTASLVEQQNKKNEISHVSTGGGASLELLEGKELPGVLALSNK 416
                              |      2        12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172  |    182      |192       202       212       222       232|     |242       252       262      |272       282       292       302       312       322       332       342 |     352       362       372       382       392       402       412    
                             -5-MSE                                                                                                                                                                             175-MSE       189-MSE                                     233-MSE |        250-MSE            269-MSE                                   311-MSE                          344-MSE                                                                    
                                                                                                                                                                                                                                                                                239-MSE                                                                                                                                                                             

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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  (1, 3)

Asymmetric Unit

(-) CATH Domains  (2, 6)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 3)

Asymmetric Unit

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (PGK_PLAF7 | P27362)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0004618    phosphoglycerate kinase activity    Catalysis of the reaction: 3-phospho-D-glycerate + ATP = 3-phospho-D-glyceroyl phosphate + ADP + H(+).
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0006096    glycolytic process    The chemical reactions and pathways resulting in the breakdown of a carbohydrate into pyruvate, with the concomitant production of a small amount of ATP and the reduction of NAD(P) to NAD(P)H. Glycolysis begins with the metabolism of a carbohydrate to generate products that can enter the pathway and ends with the production of pyruvate. Pyruvate may be converted to acetyl-coenzyme A, ethanol, lactate, or other small molecules.
    GO:0016310    phosphorylation    The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.

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 Related Entries

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        PGK_PLAF7 | P273621lgi 3oz7 3oza

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