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(-) Description

Title :  CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS L,D-TRANSPEPTIDASE 2 WITH CARBAPENEM DRUG T224
 
Authors :  G. Lamichhane, S. L. Ginell, P. Kumar
Date :  24 May 16  (Deposition) - 09 Nov 16  (Release) - 28 Dec 16  (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 (1x),B (1x)
Keywords :  Peptidase, Igd_like Domain, Ykud Domain, Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Kumar, A. Kaushik, E. P. Lloyd, S. G. Li, R. Mattoo, N. C. Ammerman, D. T. Bell, A. L. Perryman, T. A. Zandi, S. Ekins, S. L. Ginell, C. A. Townsend, J. S. Freundlich, G. Lamichhane
Non-Classical Transpeptidases Yield Insight Into New Antibacterials.
Nat. Chem. Biol. V. 13 54 2017
PubMed-ID: 27820797  |  Reference-DOI: 10.1038/NCHEMBIO.2237

(-) Compounds

Molecule 1 - L,D-TRANSPEPTIDASE 2
    Chains: A, B
    EC Number: 2.3.2.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET38A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: LDTB, LPPS, RV2518C, RVBD_2518C, P425_02624
    Organism Scientific: MYCOBACTERIUM TUBERCULOSIS (STRAIN ATCC 25618 / H37RV)
    Organism Taxid: 83332
    Strain: ATCC 25618 / H37RV
    Synonym: LDT 2,LDT(MT2)

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric Unit (2, 5)
No.NameCountTypeFull Name
16QR2Ligand/Ion(2~{S},3~{R},4~{R})-4-(1~{H}-INDOL-3-YLSULFANYL)-3-METHYL-2-[(2~{S},3~{S})-3-OXIDANYL-1-OXIDANYLIDENE-BUTAN-2-YL]-3,4-DIHYDRO-2~{H}-PYRROLE-5-CARBOXYLICACID
2GOL3Ligand/IonGLYCEROL
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
16QR1Ligand/Ion(2~{S},3~{R},4~{R})-4-(1~{H}-INDOL-3-YLSULFANYL)-3-METHYL-2-[(2~{S},3~{S})-3-OXIDANYL-1-OXIDANYLIDENE-BUTAN-2-YL]-3,4-DIHYDRO-2~{H}-PYRROLE-5-CARBOXYLICACID
2GOL2Ligand/IonGLYCEROL
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
16QR1Ligand/Ion(2~{S},3~{R},4~{R})-4-(1~{H}-INDOL-3-YLSULFANYL)-3-METHYL-2-[(2~{S},3~{S})-3-OXIDANYL-1-OXIDANYLIDENE-BUTAN-2-YL]-3,4-DIHYDRO-2~{H}-PYRROLE-5-CARBOXYLICACID
2GOL1Ligand/IonGLYCEROL
Biological Unit 3 (2, 3)
No.NameCountTypeFull Name
16QR1Ligand/Ion(2~{S},3~{R},4~{R})-4-(1~{H}-INDOL-3-YLSULFANYL)-3-METHYL-2-[(2~{S},3~{S})-3-OXIDANYL-1-OXIDANYLIDENE-BUTAN-2-YL]-3,4-DIHYDRO-2~{H}-PYRROLE-5-CARBOXYLICACID
2GOL2Ligand/IonGLYCEROL

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:213 , HIS A:214 , PHE A:215 , ILE A:291 , TRP A:394binding site for residue GOL A 501
2AC2SOFTWAREILE A:188 , LYS A:189 , ILE A:190 , GLY A:198 , PHE A:200 , TRP A:210 , HOH A:608binding site for residue GOL A 502
3AC3SOFTWAREMET A:303 , TYR A:318 , THR A:320 , GLY A:332 , HIS A:336 , TRP A:340 , SER A:351 , HIS A:352 , GLY A:353 , CYS A:354 , ASN A:356 , HOH A:665 , HOH A:694binding site for residue 6QR A 503
4AC4SOFTWAREGLU B:213 , HIS B:214 , PHE B:215 , ILE B:291binding site for residue GOL B 501
5AC5SOFTWARESER B:279 , MET B:280 , MET B:303 , TYR B:318 , GLY B:332 , PHE B:334 , HIS B:336 , TRP B:340 , SER B:351 , HIS B:352 , GLY B:353 , LEU B:355 , ASN B:356 , HOH B:605 , HOH B:727binding site for Di-peptide 6QR B 502 and CYS B 354

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5K69)

(-) 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 5K69)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5K69)

(-) Exons   (0, 0)

(no "Exon" information available for 5K69)

(-) 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:350
                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee...............eeeee..eeeeeeee........eee.....eeee........eeeeeeeeee..eeeeeeeeee.....eee.eeee....eee.....eeeee.....hhhhhhhheeeeee....eeeee....eeeeee........eeeeee..........eee...eeeeeee...eeeeee....eeeeee..eeeeeee............eeee...eeeeeeee.hhhh.........eeeeeeeee......eeee.hhhh............eeehhhhhhhhhhhh....eeeee.............hhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5k69 A  58 LVPKLTASVTDGAVGVTVDAPVSVTAADGVLAAVTMVNDNGRPVAGRLSPDGLRWSTTEQLGYNRRYTLNATALGLGGAATRQLTFQTSSPAHLTMPYVMPGDGEVVGVGEPVAIRFDENIADRGAAEKAIKITTNPPVEGAFYWLNNREVRWRPEHFWKPGTAVDVAVNTYGVDLGEGMFGEDNVQTHFTIGDEVIATADDNTKILTVRVNGEVVKSMPTSMGKDSTPTANGIYIVGSRYKHIIMDSSTYGVPVNSPNGYRTDVDWATQISYSGVFVHSAPWSVGAQGHTNTSHGCLNVSPSNAQWFYDHVKRGDIVEVVNTVGGTLPGIDGLGDWNIPWDQWRAGNAK 407
                                    67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407


Chain B from PDB  Type:PROTEIN  Length:349
                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee...............eeeee..eeeeeeee........eee.....eeee........eeeeeeeeee..eeeeeeeeee.....eee.eeee.....ee.....eeeee.....hhhhhhhheeeeee....eeeee....eeeeee........eeeeee..........eee...eeeeeee...eeeeee....eeeeee..eeeeeee............eeee...eeeeeeee.hhhh.........eeeeeeeee......eeee.hhhh............eeehhhhhhhhhhhh....eeeee.............hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5k69 B  58 LVPKLTASVTDGAVGVTVDAPVSVTAADGVLAAVTMVNDNGRPVAGRLSPDGLRWSTTEQLGYNRRYTLNATALGLGGAATRQLTFQTSSPAHLTMPYVMPGDGEVVGVGEPVAIRFDENIADRGAAEKAIKITTNPPVEGAFYWLNNREVRWRPEHFWKPGTAVDVAVNTYGVDLGEGMFGEDNVQTHFTIGDEVIATADDNTKILTVRVNGEVVKSMPTSMGKDSTPTANGIYIVGSRYKHIIMDSSTYGVPVNSPNGYRTDVDWATQISYSGVFVHSAPWSVGAQGHTNTSHGCLNVSPSNAQWFYDHVKRGDIVEVVNTVGGTLPGIDGLGDWNIPWDQWRAGNA 406
                                    67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397
   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 5K69)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5K69)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5K69)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)

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  5k69
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 Related Entries

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

UniProtKB/Swiss-Prot
        LDT2_MYCTU | I6Y9J2: 3vyn 3vyo 3vyp 4gsq 4gsr 4gsu 4hu2 4huc 4qr7 4qra 4qrb 4qtf 5d7h 5dc2 5dcc 5du7 5duj 5dvp 5dzj 5dzp 5e1g 5e1i 5lb1 5lbg

(-) Related Entries Specified in the PDB File

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