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(-) Description

Title :  CRYSTAL STRUCTURE OF CLADOSPORIN IN COMPLEX WITH HUMAN LYSYL-TRNA SYNTHETASE
 
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 :  2.10
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B,C  (2x)
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 1 2015
PubMed: search

(-) Compounds

Molecule 1 - LYSINE--TRNA LIGASE
    Chains: A, B
    EC Number: 6.1.1.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: KARS, KIAA0070
    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
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    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

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

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (3, 8)
No.NameCountTypeFull Name
1GOL4Ligand/IonGLYCEROL
2KRS2Ligand/IonCLADOSPORIN
3LYS2Mod. Amino AcidLYSINE
Biological Unit 1 (3, 16)
No.NameCountTypeFull Name
1GOL8Ligand/IonGLYCEROL
2KRS4Ligand/IonCLADOSPORIN
3LYS4Mod. Amino AcidLYSINE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:323 , GLU A:325 , HIS A:331 , ASN A:332 , PHE A:335 , THR A:337 , GLU A:494 , ILE A:495 , GLY A:550 , ARG A:553 , LYS A:602 , HOH A:757 , HOH A:863binding site for residue KRS A 601
2AC2SOFTWAREGLY A:277 , GLU A:301 , ARG A:323 , GLU A:339 , TYR A:341 , ASN A:497 , TYR A:499 , GLU A:501 , GLY A:546 , GLY A:548 , KRS A:601 , HOH A:748binding site for residue LYS A 602
3AC3SOFTWAREARG A:131 , HIS A:133 , GLY A:149 , GLU A:150 , GLY A:151 , ILE A:235 , ARG A:241 , HOH A:803 , HOH A:872 , HOH A:919binding site for residue GOL A 603
4AC4SOFTWAREASP A:445 , GLU A:453 , GLU A:487binding site for residue GOL A 604
5AC5SOFTWAREARG B:323 , GLU B:325 , HIS B:331 , ASN B:332 , PHE B:335 , THR B:337 , GLU B:494 , ILE B:495 , CYS B:496 , GLY B:550 , ARG B:553 , LYS B:602 , HOH B:826 , HOH B:896binding site for residue KRS B 601
6AC6SOFTWAREGLY B:277 , GLU B:301 , ARG B:323 , GLU B:339 , TYR B:341 , ASN B:497 , TYR B:499 , GLU B:501 , GLY B:546 , KRS B:601 , HOH B:760binding site for residue LYS B 602
7AC7SOFTWARETYR B:347 , MET B:351 , ARG B:393 , ASN B:395 , CYS B:463 , ASP B:464 , HOH B:852binding site for residue GOL B 603
8AC8SOFTWAREASP B:445 , GLU B:453 , GLU B:487 , GLU B:494 , HOH B:739binding site for residue GOL B 604

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1C:23 -C:23

(-) Cis Peptide Bonds  (5, 5)

Asymmetric Unit
No.Residues
1Gly A:219 -Leu A:220
2Pro A:389 -Pro A:390
3Pro A:436 -Pro A:437
4Pro B:389 -Pro B:390
5Pro B:436 -Pro B:437

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4YCU)

(-) 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:505
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhh.............hhhhhhhhhh............eeeeeeeeeeee....eeeeeeee..eeeeeeee.hhh.hhhhhhhhhhhh....eeeeeeeeee.....eeeeeeeeeeee..............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..ee.....ee...........eeee....eeeee...hhhhhhhhhhh...eeeeeeeee...........eeeeeeeeee..hhhhhhhhhhhhhhhhhhhhhh..eeee.........eeee.....eeeehhhhhhhhhh..........hhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhh...eeee..hhhhh..............eeeeee..eeeeeeee...hhhhhhhhhhhhhhhhh.........hhhhhhhhhh....eeeeeeehhhhhhhhh...hhhhhh........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ycu A  72 DPNQYYKIRSQAIHQLKVNGEDPYPHKFHVDISLTDFIQKYSHLQPGDHLTDITLKVAGRIHAKRASGGKLIFYDLRGEGVKLQVMANSRNYKSEEEFIHINNKLRRGDIIGVQGNPGKTKKGELSIIPYEITLLSPCLHMLPHLHFGLKDKETRYRQRYLDLILNDFVRQKFIIRSKIITYIRSFLDELGFLEIETPMMNIIPGGAVAKPFITYHNELDMNLYMRIAPELYHKMLVVGGIDRVYEIGRQFRNEGIDLTHNPEFTTCEFYMAYADYHDLMEITEKMVSGMVKHITGSYKVTYHPDGPEGQAYDVDFTPPFRRINMVEELEKALGMKLPETNLFETEETRKILDDICVAKAVECPPPRTTARLLDKLVGEFLEVTCINPTFICDHPQIMSPLAKWHRSKEGLTERFELFVMKKEICNAYTELNDPMRQRQLFEEQAKAKAAGDDEAMFIDENFCTALEYGLPPTAGWGMGIDRVAMFLTDSNNIKEVLLFPAMKPE 576
                                    81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571     


Chain B from PDB  Type:PROTEIN  Length:499
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhh.............hhhhhhhhhh............eeeeeeeeeeee....eeeeeeee..eeeeeeee.....hhhhhhhhhhhh....eeeeeeeeee.....eeeeeeeeeeee..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..ee.....ee...........eeee....eeeee...hhhhhhhhhhh...eeeeeeeee...........eeeeeeeeee..hhhhhhhhhhhhhhhhhhhhhh..eeee.........eeee.....eeeehhhhhhhhhh....hhhhh.hhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhh...eeee..hhhhh..............eeeeee..eeeeeeee...hhhhhhhhhhhhhhhhhhh.......hhhhhhhhh.....eeeeeeehhhhhhhhh...hhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ycu B  72 DPNQYYKIRSQAIHQLKVNGEDPYPHKFHVDISLTDFIQKYSHLQPGDHLTDITLKVAGRIHAKRASGGKLIFYDLRGEGVKLQVMANSRNYKSEEEFIHINNKLRRGDIIGVQGNPGKTKKGELSIIPYEITLLSPCLHMLPHLDKETRYRQRYLDLILNDFVRQKFIIRSKIITYIRSFLDELGFLEIETPMMNIIPGGAVAKPFITYHNELDMNLYMRIAPELYHKMLVVGGIDRVYEIGRQFRNEGIDLTHNPEFTTCEFYMAYADYHDLMEITEKMVSGMVKHITGSYKVTYHPDGPEGQAYDVDFTPPFRRINMVEELEKALGMKLPETNLFETEETRKILDDICVAKAVECPPPRTTARLLDKLVGEFLEVTCINPTFICDHPQIMSPLAKWHRSKEGLTERFELFVMKKEICNAYTELNDPMRQRQLFEEQAKAKAAGDDEAMFIDENFCTALEYGLPPTAGWGMGIDRVAMFLTDSNNIKEVLLFPAMKP 575
                                    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         
                                                                                                                                                                          216|                                                                                                                                                                                                                                                                                                                                                                 
                                                                                                                                                                           222                                                                                                                                                                                                                                                                                                                                                                 


Chain C from PDB  Type:PROTEIN  Length:31
                                                               
               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
                 4ycu C   2 PMYQVKPYHGGGAPLRVELPTCMYRLPNVHG  32
                                    11        21        31
   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 4YCU)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (33, 40)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

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

(-) Related Entries Specified in the PDB File

4ycv 4ycw