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(-) Description

Title :  H.INFLUENZAE TRMD IN COMPLEX WITH N-(4-{[(1H-IMIDAZOL-2-YLMETHYL) AMINO]METHYL}BENZYL)-4-OXO-3,4-DIHYDROTHIENO[2,3-D]PYRIMIDINE-5-CARBOXAMIDE
 
Authors :  N. B. Olivier, P. Hill
Date :  21 Aug 13  (Deposition) - 04 Sep 13  (Release) - 09 Oct 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.94
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Trefoil, Trmd, Sam, Sah, Sinefungin, Hmt, Structural Genomics, Trefoil Knot, Methyl Transferase To Trna, Trna, Transferase- Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. J. Hill, A. Abibi, R. Albert, B. Andrews, M. M. Gagnon, N. Gao, T. Grebe, L. I. Hajec, J. Huang, S. Livchak, S. D. Lahiri, D. C. Mckinney J. Thresher, H. Wang, N. Olivier, E. T. Buurman
Selective Inhibitors Of Bacterial T-Rna-(N(1)G37) Methyltransferase (Trmd) That Demonstrate Novel Ordering Of The Lid Domain.
J. Med. Chem. V. 56 7278 2013
PubMed-ID: 23981144  |  Reference-DOI: 10.1021/JM400718N

(-) Compounds

Molecule 1 - TRNA (GUANINE-N(1)-)-METHYLTRANSFERASE
    Chains: A, B
    EC Number: 2.1.1.228
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET SYSTEM
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: HI_0202, TRMD
    Organism Scientific: HAEMOPHILUS INFLUENZAE
    Organism Taxid: 71421
    Strain: ATCC51907
    Synonym: M1G-METHYLTRANSFERASE, TRNA [GM37] METHYLTRANSFERASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 6)

Asymmetric/Biological Unit (4, 6)
No.NameCountTypeFull Name
121W2Ligand/IonN-(4-{[(1H-IMIDAZOL-2-YLMETHYL)AMINO]METHYL}BENZYL)-4-OXO-3,4-DIHYDROTHIENO[2,3-D]PYRIMIDINE-5-CARBOXAMIDE
2ACT1Ligand/IonACETATE ION
3GOL1Ligand/IonGLYCEROL
4SO42Ligand/IonSULFATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:103 , GLN A:104 , ASN A:105 , GLN A:106 , PHE A:155 , ILE A:156 , PRO A:157 , HOH A:431 , HOH A:488 , HOH A:516BINDING SITE FOR RESIDUE GOL A 301
2AC2SOFTWAREARG A:68 , VAL A:186 , LEU A:187 , GLU A:188 , HOH A:445 , HOH A:447 , ARG B:68 , LEU B:187 , GLU B:188BINDING SITE FOR RESIDUE SO4 A 302
3AC3SOFTWARELEU A:87 , SER A:88 , PRO A:89 , TYR A:115 , GLU A:116 , SER A:132 , ILE A:133 , GLY A:134 , TYR A:136 , LEU A:138 , GLY A:140 , GLY A:141 , PRO A:144 , HOH A:408 , HOH A:580 , ASP B:169 , ALA B:172 , ASP B:173 , ASP B:177 , HOH B:538BINDING SITE FOR RESIDUE 21W A 303
4AC4SOFTWARETRP B:2 , ALA B:78BINDING SITE FOR RESIDUE ACT B 301
5AC5SOFTWAREALA B:103 , ASN B:105 , GLN B:106 , PHE B:155 , ILE B:156 , PRO B:157 , HOH B:473 , HOH B:551 , HOH B:562BINDING SITE FOR RESIDUE SO4 B 302
6AC6SOFTWARELEU B:87 , SER B:88 , PRO B:89 , GLU B:116 , SER B:132 , ILE B:133 , GLY B:134 , TYR B:136 , LEU B:138 , GLY B:140 , GLY B:141 , PRO B:144 , HOH B:625 , HOH B:650BINDING SITE FOR RESIDUE 21W B 303

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Arg A:183 -Pro A:184
2His A:201 -Glu A:202
3Ile A:204 -Arg A:205
4Arg B:183 -Pro B:184

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4MCB)

(-) 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:205
                                                                                                                                                                                                                                             
               SCOP domains d4mcba_ A: automated matches                                                                                                                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..hhhhhhhhhhhhhhhhhhhh...eeeeehhhhhh.......ee.........eehhhhhhhhhhhhhhhhh...eeeee....ee.hhhhhhhhh...eeeee.......hhhhhhhhh.eeee........hhhhhhhhhhhhhh..................ee..ee............hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4mcb A   1 MWIGVISLFPEMFKAITEFGVTGRAVKHNLLKVECWNPRDFTFDKHKTVDDRPYGGGPGMLMMVQPLRDAIHTAKAAAGEGAKVIYLSPQGRKLDQGGVTELAQNQKLILVCGRYEGIDERLIQTEIDEEWSIGDYVLTGGELPAMTLIDAVARFIPGVLGLLDCPHYTRPEVLEGLTVPPVLMSHHEEIRKWRLKQSLQRTWLR 219
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160|      183       193    || 204       214     
                                                                                                                                                                                         160|                     198|                   
                                                                                                                                                                                          174                      200                   


Chain B from PDB  Type:PROTEIN  Length:243
                                                                                                                                                                                                                                                                                   
               SCOP domains d4mcbb_ B: automated matches                                                                                                                                                                                                                        SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..hhhhhhhhhhhhhhhhhhhh...eeeeehhhhhh.......ee.........eehhhhhhhhhhhhhhhhh...eeeee....ee.hhhhhhhhh...eeeee.......hhhhhhhhh.eeee........hhhhhhhhhhhhhh..........hhhhhhh..............ee..ee.hhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4mcb B   1 MWIGVISLFPEMFKAITEFGVTGRAVKHNLLKVECWNPRDFTFDKHKTVDDRPYGGGPGMLMMVQPLRDAIHTAKAAAGEGAKVIYLSPQGRKLDQGGVTELAQNQKLILVCGRYEGIDERLIQTEIDEEWSIGDYVLTGGELPAMTLIDAVARFIPGVLGKQASAEEDSFADGLLDCPHYTRPEVLEGLTVPPVLMSGHHEEIRKWRLKQSLQRTWLRRPELLEGLALTDEQRKLLKEAQAE 243
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240
   Legend:   → Mismatch (orange background)
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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  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Arg A:183 - Pro A:184   [ RasMol ]  
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 Related Entries

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UniProtKB/Swiss-Prot
        TRMD_HAEIN | P43912: 1uaj 1uak 1ual 1uam 3axz 4mcc 4mcd 4ypw 4ypx 4ypy 4ypz 4yq0 4yq1 4yq2 4yq3 4yq4 4yq5 4yq6 4yq7 4yq8 4yq9 4yqa 4yqb 4yqc 4yqd 4yqg 4yqi 4yqj 4yqk 4yql 4yqn 4yqo 4yqp 4yqq 4yqr 4yqs 4yqt 4yvg 4yvh 4yvi 4yvj 4yvk 5d9f

(-) Related Entries Specified in the PDB File

4mcc