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(-) Description

Title :  CRYSTAL STRUCTURE OF ASPARTYL-TRNA SYNTHETASE FROM MYCOBACTERIUM SMEGMATIS WITH BOUND ASPARTIC ACID
 
Authors :  Seattle Structural Genomics Center For Infectious Disease (S
Date :  17 Dec 13  (Deposition) - 22 Jan 14  (Release) - 22 Apr 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Mycobaterium, Structural Genomics, Trna Synthetase, Asps, Asprs, Niaid, National Institute Of Allergy And Infectious Diseases, Seattle Structural Genomics Center For Infectious Disease, Ssgcid, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Baugh, I. Phan, D. W. Begley, M. C. Clifton, B. Armour, D. M. Dranow, B. M. Taylor, M. M. Muruthi, J. Abendroth, J. W. Fairman, D. Fox, S. H. Dieterich, B. L. Staker, A. S. Gardberg, R. Choi, S. N. Hewitt, A. J. Napuli, J. Myers, L. K. Barrett, Y. Zhang, M. Ferrell, E. Mundt, K. Thompkins, N. Tran, S. Lyons-Abbott, A. Abramov, A. Sekar, D. Serbzhinskiy, D. Lorimer, G. W. Buchko, R. Stacy, L. J. Stewart, T. E. Edwards, W. C. Van Voorhis, P. J. Myler
Increasing The Structural Coverage Of Tuberculosis Drug Targets.
Tuberculosis (Edinb) V. 95 142 2015
PubMed-ID: 25613812  |  Reference-DOI: 10.1016/J.TUBE.2014.12.003

(-) Compounds

Molecule 1 - ASPARTATE--TRNA LIGASE
    Chains: A, B
    EC Number: 6.1.1.12
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: ASPS, MSMEG_3003, MSMEI_2928
    Organism Scientific: MYCOBACTERIUM SMEGMATIS
    Organism Taxid: 246196
    Strain: ATCC 700084/ MC(2)155
    Synonym: ASPARTYL-TRNA SYNTHETASE, ASPRS

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric/Biological Unit (2, 6)
No.NameCountTypeFull Name
1ASP2Mod. Amino AcidASPARTIC ACID
2TRS4Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:171 , SER A:193 , GLN A:195 , LYS A:198 , ARG A:217 , GLN A:231 , HIS A:449 , HIS A:450 , GLY A:486 , ARG A:490 , ILE A:532 , ALA A:533 , HOH A:934 , HOH A:979BINDING SITE FOR RESIDUE ASP A 801
2AC2SOFTWAREASP A:282 , MET A:448 , HIS A:449 , ASP A:476BINDING SITE FOR RESIDUE TRS A 802
3AC3SOFTWAREASP A:31 , HIS A:32 , ASP A:520BINDING SITE FOR RESIDUE TRS A 803
4AC4SOFTWAREGLU B:171 , SER B:193 , GLN B:195 , LYS B:198 , ARG B:217 , GLN B:231 , HIS B:449 , HIS B:450 , GLY B:486 , ARG B:490 , ILE B:532 , ALA B:533 , HOH B:919BINDING SITE FOR RESIDUE ASP B 801
5AC5SOFTWAREPRO A:109 , TYR A:124 , ARG B:28 , ARG B:30 , HIS B:32BINDING SITE FOR RESIDUE TRS B 802
6AC6SOFTWAREGLN A:111 , ARG B:64 , ALA B:65 , HOH B:926BINDING SITE FOR RESIDUE TRS B 803

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4O2D)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Leu A:265 -Pro A:266
2Ala A:568 -Pro A:569
3Leu B:265 -Pro B:266
4Ala B:568 -Pro B:569

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4O2D)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4O2D)

(-) Exons   (0, 0)

(no "Exon" information available for 4O2D)

(-) Sequences/Alignments

Asymmetric/Biological 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:581
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhh..eeeeeeeeeeeeee..eeeeeeee..eeeeeee.hhhhhhhhh......eeeeeeeeee..............eeeeeeeeeeee.............hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh..ee.................eee.......eee....hhhhhhhhhhh...eeeeeeeee.........eeeeeeeeee..hhhhhhhhhhhhhhhhhhhhh........eeehhhhhhhhh............ee.........hhhhh..eeeeeee.hhhhhhhhhhhhhhhhhhh......eeeee.....ee..hhhhhhhhhhhhhhhhhh.....eeeeeeehhhhhhhhhhhhhhhhhhhh.........eeeee....eeehhhhhh..........eee........hhhhh.............eeeeee..eeeeeeee...hhhhhhhhhhhh..hhhhhhhhhhhhhhhh......eeeeeeehhhhhhhhhh..hhhhhh...................hhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4o2d A   2 VLRTHAAGSLRPADAGQTVTLAGWVARRRDHGGVIFIDLRDASGVSQVVFREGDVLAAAHRLRAEFCVAVTGVVEVRPEGNENPEIPTGQIEVNATELTVLGESAPLPFQLDEQAGEEARLKYRYLDLRREGPGNALRLRSKVNAAARSVLAEHDFVEIETPTLTRSTPEGARDFLVPARLQPGSFYALPQSPQLFKQLLMVAGMERYYQIARCYRDEDFDRQPEFTQLDMEMSFVEADDVIAISEQVLKAVWATIGYDLPLPLPRISYEEAMRRFGSDKPDLRFGIELVECTEYFKDTTFRVFQAPYVGAVVMPGGASQPRRTLDGWQEFAKQRGHKGLAYVLVGEDGTLGGPVAKNLSDAERDGLVAHVGANPGDCIFFAAGPAKGARALLGATRIEIAKRLDLIDPNAWAFTWVVDFPMFEAADEATAAGDVAVGSGAWTAMHHAFTAPKPDSVDTFDSDPGNALSDAYDIVCNGNEIGGGSIRIHRRDIQERVFAMMGIDHDEAQEKFGFLLDAFSYGAPPHGGIAFGWDRITALLAGVDSIREVIAFPKSGGGVDPLTDAPAPITPQQRKESGIDD 801
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221|      233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583|
                                                                                                                                                                                                                                                     221|                                                                                                                                                                                                                                                                                                                                                                    583|
                                                                                                                                                                                                                                                      224                                                                                                                                                                                                                                                                                                                                                                     801


Chain B from PDB  Type:PROTEIN  Length:516
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....hhhhhhhhhh..eeeeeeeeeeeeee..eeeeeeee..eeeeeee.hhhhhhhhh......eeeeeeeeee..............eeeeeeeeeeee.............hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh..ee.................eee.......eee....hhhhhhhhhhh...eeeeeeeee.........eeeeeeeeee..hhhhhhhhhhhhhhhhhhhhh........eeehhhhhhhhh............ee......eeee.....hhhhhhh..eeeehhhhhhhhhhhhhhhhhhhh.........eeeee....eeehhhhhh..........eee........hhhhh.............eeeeee..eeeeeeee...hhhhhhhhhhhh..hhhhhhhhhhhhhhhh......eeeeeeehhhhhhhhhh..hhhhhh...................hhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4o2d B   2 VLRTHAAGSLRPADAGQTVTLAGWVARRRDHGGVIFIDLRDASGVSQVVFREGDVLAAAHRLRAEFCVAVTGVVEVRPEGNENPEIPTGQIEVNATELTVLGESAPLPFQLDEQAGEEARLKYRYLDLRREGPGNALRLRSKVNAAARSVLAEHDFVEIETPTLTRSTPEGARDFLVPARLQPGSFYALPQSPQLFKQLLMVAGMERYYQIARCYRDEDFDRQPEFTQLDMEMSFVEADDVIAISEQVLKAVWATIGYDLPLPLPRISYEEAMRRFGSDKPDLRFGIELVECTEYFPYVGAVVMPWQEFAKQRGFFAAGPAKGARALLGATRIEIAKRLDLIDPNAWAFTWVVDFPMFEAADEATAAGDVAVGSGAWTAMHHAFTAPKPDSVDTFDSDPGNALSDAYDIVCNGNEIGGGSIRIHRRDIQERVFAMMGIDHDEAQEKFGFLLDAFSYGAPPHGGIAFGWDRITALLAGVDSIREVIAFPKSGGGVDPLTDAPAPITPQQRKESGIDD 801
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221|      233       243       253       263       273       283       293     ||313    || 335   ||  388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578    ||
                                                                                                                                                                                                                                                     221|                                                                        299|     318|     339|                                                                                                                                                                                                     583|
                                                                                                                                                                                                                                                      224                                                                         310      331      383                                                                                                                                                                                                      801
   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 4O2D)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4O2D)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4O2D)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)

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        SYDND_MYCS2 | A0QWN3: 4rmf

(-) Related Entries Specified in the PDB File

1eqr RELATED ID: SSGCID-MYSMA.00145.A RELATED DB: TARGETTRACK