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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN THRRS COMPLEXING WITH A BIOENGINEERED MACROLIDE BC194
 
Authors :  P. Fang, M. Guo
Date :  23 Jun 14  (Deposition) - 30 Sep 15  (Release) - 30 Sep 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Trna, Synthetase, Inhibitor, Macrolide, Ligase-Antibiotic Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. C. Mirando, P. Fang, T. F. Williams, L. C. Baldor, A. K. Howe, A. M. Ebert, B. Wilkinson, K. M. Lounsbury, M. Guo, C. S. Francklyn
Aminoacyl-Trna Synthetase Dependent Angiogenesis Revealed B A Bioengineered Macrolide Inhibitor.
Sci Rep V. 5 13160 2015
PubMed-ID: 26271225  |  Reference-DOI: 10.1038/SREP13160

(-) Compounds

Molecule 1 - THREONINE--TRNA LIGASE, CYTOPLASMIC
    Chains: A, B, C, D
    EC Number: 6.1.1.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 322-723
    Gene: TARS
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: THREONYL-TRNA SYNTHETASE,THRRS

 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  (2, 8)

Asymmetric Unit (2, 8)
No.NameCountTypeFull Name
1BC94Ligand/Ion(1R,2R)-2-[(2S,6E,8R,9S,11R,13S,15S,16S)-7-CYANO-8,16-DIHYDROXY-9,11,13,15-TETRAMETHYL-18-OXOOXACYCLOOCTADEC-6-EN-2-YL]CYCLOBUTANECARBOXYLICACID
2ZN4Ligand/IonZINC ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1BC92Ligand/Ion(1R,2R)-2-[(2S,6E,8R,9S,11R,13S,15S,16S)-7-CYANO-8,16-DIHYDROXY-9,11,13,15-TETRAMETHYL-18-OXOOXACYCLOOCTADEC-6-EN-2-YL]CYCLOBUTANECARBOXYLICACID
2ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1BC92Ligand/Ion(1R,2R)-2-[(2S,6E,8R,9S,11R,13S,15S,16S)-7-CYANO-8,16-DIHYDROXY-9,11,13,15-TETRAMETHYL-18-OXOOXACYCLOOCTADEC-6-EN-2-YL]CYCLOBUTANECARBOXYLICACID
2ZN-1Ligand/IonZINC ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWARESER A:386 , GLY A:387 , HIS A:388 , CYS A:413 , ARG A:442 , GLN A:460 , TYR A:540 , THR A:560 , ASP A:564 , LEU A:567 , HIS A:590binding site for residue BC9 A 801
02AC2SOFTWARECYS A:413 , HIS A:464 , HIS A:590binding site for residue ZN A 802
03AC3SOFTWAREGLY B:387 , HIS B:388 , CYS B:413 , ARG B:442 , GLN B:460 , TYR B:540 , THR B:560 , ASP B:564 , LEU B:567 , HIS B:590binding site for residue BC9 B 801
04AC4SOFTWARECYS B:413 , HIS B:464 , HIS B:590binding site for residue ZN B 802
05AC5SOFTWAREHIS C:388 , MET C:411 , CYS C:413 , ARG C:442 , TYR C:540 , THR C:560 , ASP C:564 , LEU C:567 , HIS C:590binding site for residue BC9 C 801
06AC6SOFTWARECYS C:413 , HIS C:464 , HIS C:590binding site for residue ZN C 802
07AC7SOFTWAREHIS D:388 , MET D:411 , CYS D:413 , ARG D:442 , TYR D:540 , THR D:560 , ASP D:564 , LEU D:567 , HIS D:590binding site for residue BC9 D 801
08AC8SOFTWARECYS D:413 , HIS D:464 , HIS D:590binding site for residue ZN D 802
09AC9SOFTWAREASN B:497 , LEU B:498 , SER B:499 , LEU B:532 , SER B:534 , GLY B:535 , ASP B:536binding site for Ligand ASN B 533 bound to ASN B 497
10AD1SOFTWAREILE C:662 , ARG C:663 , ASN C:664 , ALA C:665 , LEU C:667 , ALA C:668 , GLN C:669 , ARG C:689 , THR C:690 , ARG C:691 , ASP C:692 , LYS C:694 , VAL C:695binding site for Di-peptide GLN C 666 and ASN C 693
11AD2SOFTWAREILE D:662 , ARG D:663 , ASN D:664 , ALA D:665 , LEU D:667 , ALA D:668 , GLN D:669 , ARG D:689 , THR D:690 , ARG D:691 , ASP D:692 , LYS D:694binding site for Di-peptide GLN D 666 and ASN D 693

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Leu A:430 -Pro A:431
2Leu B:430 -Pro B:431
3Leu C:430 -Pro C:431
4Leu D:430 -Pro D:431

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4TTV)

(-) 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:403
                                                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhh..ee.........eehhhhhhhhhhhhhhhhhhhhhhh.ee.....eeehhhhhhhhhhhhhhhhh.eeee..eeeee...hhhhhhhhhh....hhhhh.eeeee..eee...............eee..eeeeee...hhhhhhhhhhhhhhhhhhhhh.eeeeeee........hhhhhhhhhhhhhhhhhhhh..eee..........eeeeeee.....eeeeeeeeee.hhhhhh...............eeeeee...hhhhhhhhhhhhhh...........eeeee.hhhhhhhhhhhhhhhhh....eee......hhhhhhhhhhhh...eeeeehhhhhhhheeeeee....eeeeeehhhhhhhhhhhhhh...hhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ttv A 321 SDHRKIGRDQELYFFHELSPGSCFFLPKGAYIYNALIEFIRSEYRKRGFQEVVTPNIFNSRLWMTSGHWQHYSENMFSFEVEKELFALKPMNCPGHCLMFDHRPRSWRELPLRLADFGVLHRNELSGALTGLTRVRRFQQDDAHIFCAMEQIEDEIKGCLDFLRTVYSVFGFSFKLNLSTRPEKFLGDIEVWDQAEKQLENSLNEFGEKWELNSGDGAFYGPKIDIQIKDAIGRYHQCATIQLDFQLPIRFNLTYVSHDGDDKKRPVIVHRAILGSVERMIAILTENYGGKWPFWLSPRQVMVVPVGPTCDEYAQKVRQQFHDAKFMADIDLDPGCTLNKKIRNAQLAQYNFILVVGEKEKISGTVNIRTRDNKVHGERTISETIERLQQLKEFRSKQAEEEF 723
                                   330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710       720   


Chain B from PDB  Type:PROTEIN  Length:403
                                                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhh..ee.........eehhhhhhhhhhhhhhhhhhhhhhh.ee.....eeehhhhhhh.....hhhhh.eeee..eeeee...hhhhhhhhhh....hhhhh.eeeee..eee...............eee..eeeeee...hhhhhhhhhhhhhhhhhhhhh.eeeeeee........hhhhhhhhhhhhhhhhhhhh..eeee.........eeeeeee.....eeeeeeeeeehhhhhhh...............eeeeee...hhhhhhhhhhhhhh...........eeeee.hhhhhhhhhhhhhhhhh....eee......hhhhhhhhhhhh...eeeeehhhhhhhheeeeee....eeeeeehhhhhhhhhhhhhh...hhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ttv B 321 SDHRKIGRDQELYFFHELSPGSCFFLPKGAYIYNALIEFIRSEYRKRGFQEVVTPNIFNSRLWMTSGHWQHYSENMFSFEVEKELFALKPMNCPGHCLMFDHRPRSWRELPLRLADFGVLHRNELSGALTGLTRVRRFQQDDAHIFCAMEQIEDEIKGCLDFLRTVYSVFGFSFKLNLSTRPEKFLGDIEVWDQAEKQLENSLNEFGEKWELNSGDGAFYGPKIDIQIKDAIGRYHQCATIQLDFQLPIRFNLTYVSHDGDDKKRPVIVHRAILGSVERMIAILTENYGGKWPFWLSPRQVMVVPVGPTCDEYAQKVRQQFHDAKFMADIDLDPGCTLNKKIRNAQLAQYNFILVVGEKEKISGTVNIRTRDNKVHGERTISETIERLQQLKEFRSKQAEEEF 723
                                   330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710       720   


Chain C from PDB  Type:PROTEIN  Length:403
                                                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhh..ee.........eehhhhhhhhhhhhhhhhhhhhhhh.ee.....eeehhhhhhhh....hhhhh.eeee..eeeee...hhhhhhhhhh....hhhhh.eeeee..eee...hhhhh.......eee..eeeeee...hhhhhhhhhhhhhhhhhhhhh.eeeeeee........hhhhhhhhhhhhhhhhhhhh..eeee.........eeeeeee.....eeeeeeeeeehhhhhhh...............eeeeee...hhhhhhhhhhhhhh...........eeeee.hhhhhhhhhhhhhhhhh....eee......hhhhhhhhhhhh...eeeeehhhhhhhheeeeee....eeeeeehhhhhhhhhhhhhh...hhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ttv C 321 SDHRKIGRDQELYFFHELSPGSCFFLPKGAYIYNALIEFIRSEYRKRGFQEVVTPNIFNSRLWMTSGHWQHYSENMFSFEVEKELFALKPMNCPGHCLMFDHRPRSWRELPLRLADFGVLHRNELSGALTGLTRVRRFQQDDAHIFCAMEQIEDEIKGCLDFLRTVYSVFGFSFKLNLSTRPEKFLGDIEVWDQAEKQLENSLNEFGEKWELNSGDGAFYGPKIDIQIKDAIGRYHQCATIQLDFQLPIRFNLTYVSHDGDDKKRPVIVHRAILGSVERMIAILTENYGGKWPFWLSPRQVMVVPVGPTCDEYAQKVRQQFHDAKFMADIDLDPGCTLNKKIRNAQLAQYNFILVVGEKEKISGTVNIRTRDNKVHGERTISETIERLQQLKEFRSKQAEEEF 723
                                   330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710       720   


Chain D from PDB  Type:PROTEIN  Length:403
                                                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhh..ee.........eehhhhhhhhhhhhhhhhhhhhhhh.ee.....eeehhhhhhh.....hhhhh.eeee..eeeee...hhhhhhhhhh....hhhhh.eeeee..eee...hhhhh.......eee..eeeeee...hhhhhhhhhhhhhhhhhhhhh.eeeeeee........hhhhhhhhhhhhhhhhhhhh..eeee.........eeeeeee.....eeeeeeeeee.hhhhhh...............eeeeee...hhhhhhhhhhhhhh...........eeeee.hhhhhhhhhhhhhhhhh....eee......hhhhhhhhhhhh...eeeeehhhhhhhheeeeee....eeeeeehhhhhhhhhhhhhh...hhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ttv D 321 SDHRKIGRDQELYFFHELSPGSCFFLPKGAYIYNALIEFIRSEYRKRGFQEVVTPNIFNSRLWMTSGHWQHYSENMFSFEVEKELFALKPMNCPGHCLMFDHRPRSWRELPLRLADFGVLHRNELSGALTGLTRVRRFQQDDAHIFCAMEQIEDEIKGCLDFLRTVYSVFGFSFKLNLSTRPEKFLGDIEVWDQAEKQLENSLNEFGEKWELNSGDGAFYGPKIDIQIKDAIGRYHQCATIQLDFQLPIRFNLTYVSHDGDDKKRPVIVHRAILGSVERMIAILTENYGGKWPFWLSPRQVMVVPVGPTCDEYAQKVRQQFHDAKFMADIDLDPGCTLNKKIRNAQLAQYNFILVVGEKEKISGTVNIRTRDNKVHGERTISETIERLQQLKEFRSKQAEEEF 723
                                   330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710       720
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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 4TTV)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (17, 17)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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        SYTC_HUMAN | P26639: 1wwt 4hwt 4p3n

(-) Related Entries Specified in the PDB File

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