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(-) Description

Title :  STRUCTURAL BASIS FOR THE INHIBITION OF MYCOBACTERIUM TUBERCULOSIS L,D-TRANSPEPTIDASE BY MEROPENEM, A DRUG EFFECTIVE AGAINST EXTENSIVELY DRUG-RESISTANT STRAINS
 
Authors :  H. S. Kim, J. Kim, H. N. Im, J. Y. Yoon, D. R. An, H. J. Yoon, J. Y. Kim, H. K. Mi J. Kim, J. Y. Lee, B. W. Han, S. W. Suh
Date :  28 Aug 12  (Deposition) - 27 Feb 13  (Release) - 07 Aug 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  A,B  (1x)
Keywords :  L, D-Transpeptidase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. S. Kim, J. Kim, H. N. Im, J. Y. Yoon, D. R. An, H. J. Yoon, J. Y. Kim, H. K. Min, S. -J. Kim, J. Y. Lee, B. W. Han, S. W. Suh
Structural Basis For The Inhibition Of Mycobacterium Tuberculosis L, D-Transpeptidase By Meropenem, A Drug Effective Against Extensively Drug-Resistant Strains
Acta Crystallogr. , Sect. D V. 69 420 2013
PubMed-ID: 23519417  |  Reference-DOI: 10.1107/S0907444912048998

(-) Compounds

Molecule 1 - PROBABLE CONSERVED LIPOPROTEIN LPPS
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 131-408
    Gene: LPPS
    Organism Scientific: MYCOBACTERIUM TUBERCULOSIS
    Organism Taxid: 1773
    Synonym: LDTMT2

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B
Biological Unit 3 (1x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1DWZ2Ligand/Ion(2S,3R,4S)-4-{[(3S,5S)-5-(DIMETHYLCARBAMOYL)PYRROLIDIN-3-YL]SULFANYL}-2-[(1S,2R)-1-FORMYL-2-HYDROXYPROPYL]-3-METHYL-3,4-DIHYDRO-2H-PYRROLE-5-CARBOXYLIC ACID
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1DWZ1Ligand/Ion(2S,3R,4S)-4-{[(3S,5S)-5-(DIMETHYLCARBAMOYL)PYRROLIDIN-3-YL]SULFANYL}-2-[(1S,2R)-1-FORMYL-2-HYDROXYPROPYL]-3-METHYL-3,4-DIHYDRO-2H-PYRROLE-5-CARBOXYLIC ACID
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1DWZ1Ligand/Ion(2S,3R,4S)-4-{[(3S,5S)-5-(DIMETHYLCARBAMOYL)PYRROLIDIN-3-YL]SULFANYL}-2-[(1S,2R)-1-FORMYL-2-HYDROXYPROPYL]-3-METHYL-3,4-DIHYDRO-2H-PYRROLE-5-CARBOXYLIC ACID
Biological Unit 3 (1, 2)
No.NameCountTypeFull Name
1DWZ2Ligand/Ion(2S,3R,4S)-4-{[(3S,5S)-5-(DIMETHYLCARBAMOYL)PYRROLIDIN-3-YL]SULFANYL}-2-[(1S,2R)-1-FORMYL-2-HYDROXYPROPYL]-3-METHYL-3,4-DIHYDRO-2H-PYRROLE-5-CARBOXYLIC ACID

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREMET A:303 , TYR A:308 , TYR A:318 , VAL A:333 , HIS A:352 , GLY A:353 , CYS A:354 , HOH A:692 , HOH A:695BINDING SITE FOR RESIDUE DWZ A 501
2AC2SOFTWARETHR A:145 , MET B:303 , TYR B:308 , TYR B:318 , GLY B:332 , HIS B:352 , GLY B:353 , CYS B:354BINDING SITE FOR RESIDUE DWZ B 501

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Met A:157 -Pro A:158
2Asn A:193 -Pro A:194
3Met B:157 -Pro B:158
4Asn B:193 -Pro B:194

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4GSU)

(-) 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:268
                                                                                                                                                                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........ee.eeee.....ee.....eeeee.....hhhhhhhheeeeee....eeeee....eeeeee........eeeeeee..........ee..eeeeeeee...eeeeee....eeeeee..eeeeeee............eeee...eeeeeeee.hhhh.........eeeeeeeee......eeee.hhhh............eeehhhhhhhhhhhh....eeeee.............hhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gsu A 141 LTFQTSSPAHLTMPYVMPGDGEVVGVGEPVAIRFDENIADRGAAEKAIKITTNPPVEGAFYWLNNREVRWRPEHFWKPGTAVDVAVNTYGVDLGEGMFGEDNVQTHFTIGDEVIATADDNTKILTVRVNGEVVKSMPTSMGKDSTPTANGIYIVGSRYKHIIMDSSTYGVPVNSPNGYRTDVDWATQISYSGVFVHSAPWSVGAQGHTNTSHGCLNVSPSNAQWFYDHVKRGDIVEVVNTVGGTLPGIDGLGDWNIPWDQWRAGNAKA 408
                                   150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400        


Chain B from PDB  Type:PROTEIN  Length:268
                                                                                                                                                                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee........eeee....eee.....eeeee.....hhhhhhhheeeeee....eeeeeee..eeeeee........eeeeeee..............eeeeeeee...eeeeee....eeeeee..eeeeeee............eeee...eeeeeeee.hhh..........eeeeeeeee......eeee.hhhh............eeehhhhhhhhhhhh....eeeee.............hhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gsu B 141 LTFQTSSPAHLTMPYVMPGDGEVVGVGEPVAIRFDENIADRGAAEKAIKITTNPPVEGAFYWLNNREVRWRPEHFWKPGTAVDVAVNTYGVDLGEGMFGEDNVQTHFTIGDEVIATADDNTKILTVRVNGEVVKSMPTSMGKDSTPTANGIYIVGSRYKHIIMDSSTYGVPVNSPNGYRTDVDWATQISYSGVFVHSAPWSVGAQGHTNTSHGCLNVSPSNAQWFYDHVKRGDIVEVVNTVGGTLPGIDGLGDWNIPWDQWRAGNAKA 408
                                   150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400
   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  (0, 0)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (14, 22)

Asymmetric Unit(hide GO term definitions)

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  4gsu
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  LDT2_MYCTU | I6Y9J2
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 Related Entries

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

UniProtKB/Swiss-Prot
        LDT2_MYCTO | O53223: 3tur 3tx4 3u1p 3u1q 3vae 3vyn 3vyo 3vyp 4gsq 4gsr 4hu2 4huc 5d7h 5dc2 5dcc 5du7 5duj 5lbg
        LDT2_MYCTU | I6Y9J2: 3vyn 3vyo 3vyp 4gsq 4gsr 4hu2 4huc 4qr7 4qra 4qrb 4qtf 5d7h 5dc2 5dcc 5du7 5duj 5dvp 5dzj 5dzp 5e1g 5e1i 5k69 5lb1 5lbg

(-) Related Entries Specified in the PDB File

4gsq 4gsr