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(-) Description

Title :  CRYSTAL STRUCTURE OF CLADOSPORIN IN COMPLEX WITH PLASMODIUM LYSYL-TRNA SYNTHETASE
 
Authors :  P. Fang, J. Wang, M. Guo
Date :  20 Feb 15  (Deposition) - 24 Jun 15  (Release) - 01 Jul 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.41
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Inhibitor, Complex, Lysrs, Cladosporin, Ligase-Ligase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Fang, H. Han, J. Wang, K. Chen, X. Chen, M. Guo
Structural Basis For Specific Inhibition Of Trna Synthetase By An Atp Competitive Inhibitor.
Chem. Biol. V. 22 734 2015
PubMed-ID: 26074468  |  Reference-DOI: 10.1016/J.CHEMBIOL.2015.05.007

(-) Compounds

Molecule 1 - LYSINE--TRNA LIGASE
    Chains: A, B, C, D
    EC Number: 6.1.1.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: PFNF54_04763
    Organism Scientific: PLASMODIUM FALCIPARUM (ISOLATE NF54)
    Organism Taxid: 5843
    Strain: ISOLATE NF54
    Synonym: LYSYL-TRNA SYNTHETASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1KRS4Ligand/IonCLADOSPORIN
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1KRS2Ligand/IonCLADOSPORIN
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1KRS2Ligand/IonCLADOSPORIN

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:332 , THR A:337 , HIS A:338 , ASN A:339 , PHE A:342 , GLU A:500 , VAL A:501 , LEU A:555 , ARG A:559 , ILE A:570binding site for residue KRS A 601
2AC2SOFTWAREARG B:330 , THR B:337 , HIS B:338 , ASN B:339 , PHE B:342 , GLU B:500 , VAL B:501 , GLY B:556 , ARG B:559binding site for residue KRS B 601
3AC3SOFTWAREARG C:330 , HIS C:338 , ASN C:339 , PHE C:342 , GLU C:500 , VAL C:501 , ASN C:503 , GLY C:554 , LEU C:555 , ARG C:559binding site for residue KRS C 601
4AC4SOFTWAREARG D:330 , GLU D:332 , HIS D:338 , ASN D:339 , PHE D:342 , VAL D:501 , GLY D:554 , GLY D:556 , ARG D:559binding site for residue KRS D 601

(-) SS Bonds  (4, 4)

Asymmetric Unit
No.Residues
1A:517 -A:540
2B:517 -B:540
3C:517 -C:540
4D:517 -D:540

(-) Cis Peptide Bonds  (15, 15)

Asymmetric Unit
No.Residues
1Lys A:228 -Asp A:229
2Pro A:396 -Pro A:397
3Glu A:416 -Gln A:417
4Asn A:441 -Pro A:442
5Lys B:228 -Asp B:229
6Pro B:396 -Pro B:397
7Glu B:416 -Gln B:417
8Ser C:145 -Gly C:146
9Pro C:396 -Pro C:397
10Gln C:417 -Pro C:418
11Asn C:441 -Pro C:442
12Lys D:228 -Asp D:229
13Pro D:396 -Pro D:397
14Gln D:417 -Pro D:418
15Asn D:441 -Pro D:442

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4YCV)

(-) 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:485
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhh.............hhhhhhhhhh............eeeeeeeeeee...eeeeeeee..eeeeeeee....hhhhhhhhhhhhh.....eeeeeeeeee.....eeeeeeeeeeee...............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..ee.....ee........eeee....eeeee...hhhhhhhhhhh...eeeeeeeee...........eeeeeeeeee..hhhhhhhhhhhhhhhhhhhhhh..eeee.........eeee......eeehhhhhhhhh.........hhhhhhhhhhhhhhh........hhhhhhhhhhhhhh........eeee.....................eeeeee..eeeeeeee...............hhhhhhhhhh....eeeee.hhhhhhhhhh................ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ycv A  78 VDPRLYFENRSKFIQDQKDKGINPYPHKFERTISIPEFIEKYKDLGNGEHLEDTILNITGRIMRVSAQKLRFFDLVGDGEKIQVLANYSFHNHEKGNFAECYDKIRRGDIVGIVGFPGKSKKGELSIFPKETILLSACLHMLPMKYGLKDTEIRYRQRYLDLLINESSRHTFVTRTKIINFLRNFLNERGFFEVETPMMNLIANARPFITHHNDLDLDLYLRIATELPLKMLIVGGIDKVYEIGKVFRNEGIDNTHNPEFTSCEFYWAYADYNDLIKWSEDFFSQLVYHLFGTYKISYNKDGPENQPIEIDFTPPYPKVSIVEEIEKVTNTILEQPFDSNETIEKMINIIKEHKIELPNPPTAAKLLDQLASHFIENKYNDKPFFIVEHPQIMSPLAKYHRTKPGLTERLEMFICGKEVLNAYTELNDPFKQKECFKLLDSAFCTSLEYGLPPTGGLGLGIDRITMFLTNKNSIKDVILFPTMRP 581
                                    87        97       107       117       127       137      |149       159       169       179       189       199       209       219       229       239       249       259       269       279  ||   292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       536       546       556       566       576     
                                                                                            144|                                                                                                                                    282|                                                                                                                                                                                                                                       520|                                              
                                                                                             147                                                                                                                                     286                                                                                                                                                                                                                                        535                                              


Chain B from PDB  Type:PROTEIN  Length:486
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhh.............hhhhhhhhhh............eeeeeee.......eeeeeeee..eeeeeeee.........hhhhhhhh.....eeeeeeeeee.....eeeeeeeeeeee...............hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh...ee.....ee..........eeeee....eeeee...hhhhhhhhhhh...eeeeeeeee...........eeeeeeeeee..hhhhhhhhhhhhhhhhhhhhhh..eeee.........eeee......eeehhhhhhhhhh........hhhhhhhhhhhhhhh........hhhhhhhhhhhhhh........eeee.....................eeeeee..eeeeeeee.............hhhhhhhhhh...eeeeeeehhhhhhhhhh..hhhhh........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4ycv B  77 EVDPRLYFENRSKFIQDQKDKGINPYPHKFERTISIPEFIEKYKDLGNGEHLEDTILNITGRIMRVSAQKLRFFDLVGDGEKIQVLANYSFHNHEKGNFAECYDKIRRGDIVGIVGFPGKSKKGELSIFPKETILLSACLHMLPMKYGLKDTEIRYRQRYLDLLINESSRHTFVTRTKIINFLRNFLNERGFFEVETPMMNLIAGGANARPFITHHNDLDLDLYLRIATELPLKMLIVGGIDKVYEIGKVFRNEGIDNTHNPEFTSCEFYWAYADYNDLIKWSEDFFSQLVYHLFGTYKISYNKDGPENQPIEIDFTPPYPKVSIVEEIEKVTNTILEQPFDSNETIEKMINIIKEHKIELPNPPTAAKLLDQLASHFIENKYNDKPFFIVEHPQIMSPLAKYHRTKPGLTERLEMFICGKEVLNAYTELNDPFKQKECFDSAFCTSLEYGLPPTGGLGLGIDRITMFLTNKNSIKDVILFPTMRP 581
                                    86        96       106       116       126       136       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       418       428       438       448       458       468       478       488       498       508       518|      545       555       565       575      
                                                                                             144|                                                                                                                                                                                                                                                                                                                                                                                518|                                             
                                                                                              147                                                                                                                                                                                                                                                                                                                                                                                 536                                             


Chain C from PDB  Type:PROTEIN  Length:485
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhh.............hhhhhhhhh......ee.....eeeeeeeeee......eeeeeeee..eeeeeeee....hhhhhhhhhhhh.....eeeeeeeeeee....eeeeeeeeeeee...............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..ee.....ee........eeeee....eeeee...hhhhhhhhhhhh..eeeeeeeee...........eeeeeeeeee..hhhhhhhhhhhhhhhhhhhhhh..eeee.........eeee......eeehhhhhhhh..........hhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhh........eeee.....................eeeee....eeeeeeee............hhhhhhhhhh....eeeee.hhhhhhhhhh................ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ycv C  78 VDPRLYFENRSKFIQDQKDKGINPYPHKFERTISIPEFIEKYKDLGNGEHLEDTILNITGRIMRVSASGQKLRFFDLVGDGEKIQVLANYSFHNHEKGNFAECYDKIRRGDIVGIVGFPGKSKKELSIFPKETILLSACLHMLPMKYGLKDTEIRYRQRYLDLLINESSRHTFVTRTKIINFLRNFLNERGFFEVETPMMNLIAANARPFITHHNDLDLDLYLRIATELPLKMLIVGGIDKVYEIGKVFRNEGIDNTHNPEFTSCEFYWAYADYNDLIKWSEDFFSQLVYHLFGTYKISYNKDGPENQPIEIDFTPPYPKVSIVEEIEKVTNTILEQPFDSNETIEKMINIIKEHKIELPNPPTAAKLLDQLASHFIENKYNDKPFFIVEHPQIMSPLAKYHRTKPGLTERLEMFICGKEVLNAYTELNDPFKQKECFLDSAFCTSLEYGLPPTGGLGLGIDRITMFLTNKNSIKDVILFPTMRP 581
                                    87        97       107       117       127       137       147       157       167       177       187       197   ||  208       218       228       238       248       258       268       278   ||  290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       536       546       556       566       576     
                                                                                                                                                     201|                                                                            282|                                                                                                                                                                                                                                      518|                                              
                                                                                                                                                      203                                                                             285                                                                                                                                                                                                                                       535                                              


Chain D from PDB  Type:PROTEIN  Length:479
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh..............hhhhhhhhhh............eeeeeeeeee.....eeeeeeee..eeeeeeee....hhhhhhhhhhhhhh....eeeeeeeee......eeeeeeeeeee...............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..ee.....ee......eeee.hhhh.eeee...hhhhhhhhhhhh..eeeeeeeee...........eeeeeeeeee..hhhhhhhhhhhhhhhhhhhhhh..eeee.........eeee......eeehhhhhhhhhh.........hhhhhhhhhhhhhh........hhhhhhhhhhhhhhh.......eeee.....................eeeeee..eeeeeeeee............hhhhhhhh....eeeeeeehhhhhhhhhh..hhhhh........ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ycv D  79 DPRLYFENRSKFIQDQKDKGINPYPHKFERTISIPEFIEKYKDLGNGEHLEDTILNITGRIMRVSAGQKLRFFDLVGDGEKIQVLANYSFHNHEKGNFAECYDKIRRGDIVGIVGFPGKSKGELSIFPKETILLSACLHMLPMKYGLKDTEIRYRQRYLDLLINESSRHTFVTRTKIINFLRNFLNERGFFEVETPMMNLINARPFITHHNDLDLDLYLRIATELPLKMLIVGGIDKVYEIGKVFRNEGIDNTHNPEFTSCEFYWAYADYNDLIKWSEDFFSQLVYHLFGTYKISYNKDGPENQPIEIDFTPPYPKVSIVEEIEKVTNTILEQPFDSNETIEKMINIIKEHKIELPNPPTAAKLLDQLASHFIENKYNDKPFFIVEHPQIMSPLAKYHRTKPGLTERLEMFICGKEVLNAYTELNDPFKQKECFSAFCTSLEYGLPPTGGLGLGIDRITMFLTNKNSIKDVILFPTMRP 581
                                    88        98       108       118       128       138     ||149       159       169       179       189       199||     210       220       230       240       250       260       270       280||     294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514   ||  542       552       562       572         
                                                                                           144|                                                   200|                                                                            281|                                                                                                                                                                                                                                     518|                                            
                                                                                            146                                                    202                                                                             286                                                                                                                                                                                                                                      537
   Legend:   → Mismatch (orange background)
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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 4YCV)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (9, 9)

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  4ycv
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 Related Entries

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(-) Related Entries Specified in the PDB File

4ycu 4ycw