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(-) Description

Title :  CRYSTAL STRUCTURE OF CLADOSPORIN IN COMPLEX WITH PLASMODIUM LIKE HUMAN LYSYL-TRNA SYNTHETASE MUTANT
 
Authors :  P. Fang, J. Wang, M. Guo
Date :  20 Feb 15  (Deposition) - 10 Jun 15  (Release) - 10 Jun 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H
Biol. Unit 1:  A,B,C,D  (1x)
Biol. Unit 2:  E,F,G,H  (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 Atp Competitive Inhibitor
Chem. Biol. V. 22 1 2015
PubMed: search

(-) Compounds

Molecule 1 - LYSINE--TRNA LIGASE
    Chains: A, B, E, F
    EC Number: 6.1.1.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 98-609
    Gene: KARS, KIAA0070
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: LYSYL-TRNA SYNTHETASE,LYSRS
 
Molecule 2 - AMINOACYL TRNA SYNTHASE COMPLEX-INTERACTING MULTIFUNCTIONAL PROTEIN 2
    Chains: C, D, G, H
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 1-36
    Gene: AIMP2, JTV1, PRO0992
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: MULTISYNTHASE COMPLEX AUXILIARY COMPONENT P38,PROTEIN JTV-1

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : ABCDEFGH
Biological Unit 1 (1x): ABCD    
Biological Unit 2 (1x):     EFGH

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric Unit (2, 8)
No.NameCountTypeFull Name
1KRS4Ligand/IonCLADOSPORIN
2LYS4Mod. Amino AcidLYSINE
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1KRS2Ligand/IonCLADOSPORIN
2LYS2Mod. Amino AcidLYSINE
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
1KRS2Ligand/IonCLADOSPORIN
2LYS2Mod. Amino AcidLYSINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:323 , GLU A:325 , HIS A:331 , ASN A:332 , PHE A:335 , GLU A:494 , ILE A:495 , CYS A:496 , ASN A:497 , GLY A:550 , ARG A:553binding site for residue KRS A 602
2AC2SOFTWAREARG B:323 , GLU B:325 , THR B:330 , HIS B:331 , ASN B:332 , PHE B:335 , GLU B:494 , ILE B:495 , CYS B:496 , ASN B:497 , GLY B:550 , ARG B:553binding site for residue KRS B 602
3AC3SOFTWAREGLU E:325 , ASN E:332 , PHE E:335 , SER E:337 , ASN E:497 , GLY E:550 , ARG E:553binding site for residue KRS E 602
4AC4SOFTWAREARG F:323 , GLU F:325 , HIS F:331 , ASN F:332 , PHE F:335 , SER F:337 , ILE F:495 , CYS F:496 , ASN F:497 , GLY F:550 , ARG F:553binding site for residue KRS F 602

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (9, 9)

Asymmetric Unit
No.Residues
1Pro A:389 -Pro A:390
2Pro A:436 -Pro A:437
3His B:215 -Leu B:216
4Pro B:389 -Pro B:390
5Pro B:436 -Pro B:437
6Pro E:389 -Pro E:390
7Pro E:436 -Pro E:437
8Pro F:389 -Pro F:390
9Pro F:436 -Pro F:437

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4YCW)

(-) 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:502
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhh.............hhhhhhhhhh............eeeeeeeeeeeeee..eeeeeeee..eeeeeeee.....hhhhhhhhhhhh....eeeeeeeeee.....eeeeeeeeeeee...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..ee.....ee...........eee......eeee...hhhhhhhhhhh...eeeeeeeee...........eeeeeeeeee..hhhhhhhhhhhhhhhhhhhhhh..eeee.........eeee.....eeeehhhhhhhhhh....hhhhh.hhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhh...eeee..hhhhh..............eeeeee..eeeeeeee...hhhhhhhhhhhhhhhhhhh.......hhhhhhhhhh....eeeeeeehhhhhhhhh...hhhhh......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ycw A  72 DPNQYYKIRSQAIHQLKVNGEDPYPHKFHVDISLTDFIQKYSHLQPGDHLTDITLKVAGRIHAKRASGGKLIFYDLRGEGVKLQVMANSRNYKSEEEFIHINNKLRRGDIIGVQGNPGKTKKGELSIIPYEITLLSPCLHMLPHLLKDKETRYRQRYLDLILNDFVRQKFIIRSKIITYIRSFLDELGFLEIETPMMNIIPGGAVAKPFITYHNELDMNLYMRIATELYHKMLVVGGIDRVYEIGRVFRNEGIDLTHNPEFTSCEFYMAYADYHDLMEITEKMVSGMVKHITGSYKVTYHPDGPEGQAYDVDFTPPFRRINMVEELEKALGMKLPETNLFETEETRKILDDICVAKAVECPPPRTTARLLDKLVGEFLEVTCINPTFICDHPQIMSPLAKWHRSKEGLTERFELFVMKKEICNAYTELNDPMRQRQLFEEQAKAKAAGDDEAMFIDENFCTALEYGLPPTAGWGMGIDRVAMFLTDSNNIKEVLLFPAMKPK 601
                                    81        91       101       111       121       131       141       151       161       171       181       191       201       211    || 224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574||
                                                                                                                                                                          216|                                                                                                                                                                                                                                                                                                                                                                575|
                                                                                                                                                                           220                                                                                                                                                                                                                                                                                                                                                                 601


Chain B from PDB  Type:PROTEIN  Length:502
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhh.............hhhhhhhhhh............eeeeeeeeeeee....eeeeeeee..eeeeeeee.....hhhhhhhhhhhh....eeeeeeeeee.....eeeeeeeeeeee...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..ee.....ee...........eeee....eeeee...hhhhhhhhhhh...eeeeeeeee...........eeeeeeeeee..hhhhhhhhhhhhhhhhhhhhhh..eeee.........eeee.....eeeehhhhhhhhhh....hhhhh.hhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhh...eeee..hhhhh..............eeeeee..eeeeeeee...hhhhhhhhhhhhhhhhh.........hhhhhhhhhh....eeeeeeehhhhhhhhh...hhhhh......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ycw B  72 DPNQYYKIRSQAIHQLKVNGEDPYPHKFHVDISLTDFIQKYSHLQPGDHLTDITLKVAGRIHAKRASGGKLIFYDLRGEGVKLQVMANSRNYKSEEEFIHINNKLRRGDIIGVQGNPGKTKKGELSIIPYEITLLSPCLHMLPHLLKDKETRYRQRYLDLILNDFVRQKFIIRSKIITYIRSFLDELGFLEIETPMMNIIPGGAVAKPFITYHNELDMNLYMRIATELYHKMLVVGGIDRVYEIGRVFRNEGIDLTHNPEFTSCEFYMAYADYHDLMEITEKMVSGMVKHITGSYKVTYHPDGPEGQAYDVDFTPPFRRINMVEELEKALGMKLPETNLFETEETRKILDDICVAKAVECPPPRTTARLLDKLVGEFLEVTCINPTFICDHPQIMSPLAKWHRSKEGLTERFELFVMKKEICNAYTELNDPMRQRQLFEEQAKAKAAGDDEAMFIDENFCTALEYGLPPTAGWGMGIDRVAMFLTDSNNIKEVLLFPAMKPK 601
                                    81        91       101       111       121       131       141       151       161       171       181       191       201       211    || 224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574||
                                                                                                                                                                          216|                                                                                                                                                                                                                                                                                                                                                                575|
                                                                                                                                                                           220                                                                                                                                                                                                                                                                                                                                                                 601


Chain C from PDB  Type:PROTEIN  Length:9
                                         
               SCOP domains --------- SCOP domains
               CATH domains --------- CATH domains
               Pfam domains --------- Pfam domains
         Sec.struct. author ......... Sec.struct. author
                 SAPs(SNPs) --------- SAPs(SNPs)
                    PROSITE --------- PROSITE
                 Transcript --------- Transcript
                 4ycw C   2 PMYQVKPYH  10


Chain D from PDB  Type:PROTEIN  Length:9
                                         
               SCOP domains --------- SCOP domains
               CATH domains --------- CATH domains
               Pfam domains --------- Pfam domains
         Sec.struct. author ......... Sec.struct. author
                 SAPs(SNPs) --------- SAPs(SNPs)
                    PROSITE --------- PROSITE
                 Transcript --------- Transcript
                 4ycw D   2 PMYQVKPYH  10


Chain E from PDB  Type:PROTEIN  Length:500
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhh................hhhhhh.............eeeeeeeeeeee....eeeeeeee..eeeeeeee.....hhhhhhhhhhhh....eeeeeeeeee.....eeeeeeeeeeee..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..ee.....ee...........eeee....eeeee...hhhhhhhhhhh...eeeeeeeee...........eeeeeeeeee..hhhhhhhhhhhhhhhhhhhhhh..eeee.........eeee.....eeeehhhhhhhhhh....hhhhh.hhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhh.......eeee..hhhhh..............eeeeee..eeeeeeee...hhhhhhhhhhhhhhhhhh........hhhhhhhhhh....eeeeeeehhhhhhhhhh..hhhhh......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ycw E  72 DPNQYYKIRSQAIHQLKVNGEDPYPHKFHVDISLTDFIQKYSHLQPGDHLTDITLKVAGRIHAKRASGGKLIFYDLRGEGVKLQVMANSRNYKSEEEFIHINNKLRRGDIIGVQGNPGKTKKGELSIIPYEITLLSPCLHMLPHLDKETRYRQRYLDLILNDFVRQKFIIRSKIITYIRSFLDELGFLEIETPMMNIIPGGAVAKPFITYHNELDMNLYMRIATELYHKMLVVGGIDRVYEIGRVFRNEGIDLTHNPEFTSCEFYMAYADYHDLMEITEKMVSGMVKHITGSYKVTYHPDGPEGQAYDVDFTPPFRRINMVEELEKALGMKLPETNLFETEETRKILDDICVAKAVECPPPRTTARLLDKLVGEFLEVTCINPTFICDHPQIMSPLAKWHRSKEGLTERFELFVMKKEICNAYTELNDPMRQRQLFEEQAKAKAAGDDEAMFIDENFCTALEYGLPPTAGWGMGIDRVAMFLTDSNNIKEVLLFPAMKPK 601
                                    81        91       101       111       121       131       141       151       161       171       181       191       201       211    || 226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       601
                                                                                                                                                                          216|                                                                                                                                                                                                                                                                                                                                                              575|
                                                                                                                                                                           222                                                                                                                                                                                                                                                                                                                                                               601


Chain F from PDB  Type:PROTEIN  Length:499
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhh.............hhhhhhhhhh............eeeeeee...ee....eeeeeeee..eeeeeeee.....hhhhhhhhhhhh....eeeeeeeeee.....eeeeeeeeeeee..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..ee.....ee...........eeee....eeeee...hhhhhhhhhhh...eeeeeeeee...........eeeeeeeeee..hhhhhhhhhhhhhhhhhhhhhh..eeee.........eeee.....eeeehhhhhhhhh.....hhhhh.hhhhhhhhhhhhhhhh......hhhhhhhhhhhhhh.......eeee..hhhhh..............eeeeee..eeeeeeee...hhhhhhhhhhhhhhhhh.........hhhhhhhhhh....eeeeeeehhhhhhhhh...hhhhh......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ycw F  72 DPNQYYKIRSQAIHQLKVNGEDPYPHKFHVDISLTDFIQKYSHLQPGDHLTDITLKVAGRIHAKRASGGKLIFYDLRGEGVKLQVMANSRNYKSEEEFIHINNKLRRGDIIGVQGNPGKTKKGELSIIPYEITLLSPCLHMLPHLDKETRYRQRYLDLILNDFVRQKFIIRSKIITYIRSFLDELGFLEIETPMMNIIPGGAVAKPFITYHNELDMNLYMRIATELYHKMLVVGGIDRVYEIGRVFRNEGIDLTHNPEFTSCEFYMAYADYHDLMEITEKMVSGMVKHITGSYKVTYHPDGPEGQAYDVDFTPPFRRINMVEELEKALGMKLPETNLFETEETRKILDDICVAKAECPPPRTTARLLDKLVGEFLEVTCINPTFICDHPQIMSPLAKWHRSKEGLTERFELFVMKKEICNAYTELNDPMRQRQLFEEQAKAKAAGDDEAMFIDENFCTALEYGLPPTAGWGMGIDRVAMFLTDSNNIKEVLLFPAMKPK 601
                                    81        91       101       111       121       131       141       151       161       171       181       191       201       211    || 226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426    || 437       447       457       467       477       487       497       507       517       527       537       547       557       567       ||
                                                                                                                                                                          216|                                                                                                                                                                                                              431|                                                                                                                                           575|
                                                                                                                                                                           222                                                                                                                                                                                                               433                                                                                                                                            601


Chain G from PDB  Type:PROTEIN  Length:9
                                         
               SCOP domains --------- SCOP domains
               CATH domains --------- CATH domains
               Pfam domains --------- Pfam domains
         Sec.struct. author ......... Sec.struct. author
                 SAPs(SNPs) --------- SAPs(SNPs)
                    PROSITE --------- PROSITE
                 Transcript --------- Transcript
                 4ycw G   2 PMYQVKPYH  10


Chain H from PDB  Type:PROTEIN  Length:9
                                         
               SCOP domains --------- SCOP domains
               CATH domains --------- CATH domains
               Pfam domains --------- Pfam domains
         Sec.struct. author ......... Sec.struct. author
                 SAPs(SNPs) --------- SAPs(SNPs)
                    PROSITE --------- PROSITE
                 Transcript --------- Transcript
                 4ycw H   2 PMYQVKPYH  10
   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  (0, 0)

(no "SCOP Domain" information available for 4YCW)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (33, 40)

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 Related Entries

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

UniProtKB/Swiss-Prot
        AIMP2_HUMAN | Q13155: 4dpg 4ycu 5a1n 5a34 5a5h
        SYK_HUMAN | Q15046: 3bju 4dpg 4ycu

(-) Related Entries Specified in the PDB File

4ycu 4ycv