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(-) Description

Title :  X-RAY CRYSTAL STRUCTURE OF L,D TRANSPEPTIDASE 2 FROM MYCOBACTERIUM TUBERCULOSIS
 
Authors :  H. Saavedra, L. A. Basta, G. Lamichhane, M. A. Bianchet
Date :  13 Aug 15  (Deposition) - 28 Sep 16  (Release) - 28 Sep 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.49
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Pan, L. A. Basta, E. P. Lloyd, R. Mattoo, H. Saavedra, J. Jean, C. A. Townsend, M. A. Bianchet, G. Lamichhane
Molecular Structures And Mechanism Of Inhibition Of Mycobacterium Tuberculosis L, D-Transpeptidase By Tebipenem And Biapenem
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - L,D-TRANSPEPTIDASE 2
    Chains: A, B
    EC Number: 2.3.2.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: LDTB, MT2594, V735_02606
    Organism Scientific: MYCOBACTERIUM TUBERCULOSIS
    Organism Taxid: 83331
    Strain: CDC 1551 / OSHKOSH
    Synonym: LDT 2,LDT(MT2)

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 18)

Asymmetric Unit (2, 18)
No.NameCountTypeFull Name
1GOL5Ligand/IonGLYCEROL
2SO413Ligand/IonSULFATE ION
Biological Unit 1 (2, 9)
No.NameCountTypeFull Name
1GOL3Ligand/IonGLYCEROL
2SO46Ligand/IonSULFATE ION
Biological Unit 2 (2, 9)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2SO47Ligand/IonSULFATE ION

(-) Sites  (18, 18)

Asymmetric Unit (18, 18)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:104 , PRO A:107 , SO4 A:505 , HOH A:619binding site for residue SO4 A 501
02AC2SOFTWAREGLY A:234 , GLU A:235 , HOH A:610binding site for residue SO4 A 502
03AC3SOFTWAREARG A:99 , GLU A:116 , ARG A:122 , PRO B:311 , VAL B:312 , ASN B:313binding site for residue SO4 A 503
04AC4SOFTWAREARG A:297 , ARG A:371 , HOH A:604binding site for residue SO4 A 504
05AC5SOFTWARESER A:106 , ARG A:111 , SO4 A:501binding site for residue SO4 A 505
06AC6SOFTWAREHIS A:336 , TRP A:340 , SER A:351 , HIS A:352 , CYS A:354 , ASN A:356binding site for residue GOL A 506
07AC7SOFTWAREASN A:177 , ASN A:204 , ASN A:205 , HOH A:605binding site for residue GOL A 507
08AC8SOFTWAREGLU A:176 , ARG A:206binding site for residue GOL A 508
09AC9SOFTWAREHIS A:300 , HIS B:150binding site for residue SO4 A 509
10AD1SOFTWAREARG B:297 , ARG B:371 , HOH B:604 , HOH B:628 , HOH B:690binding site for residue SO4 B 501
11AD2SOFTWAREASN B:177 , ASN B:205 , ARG B:206 , HOH B:613 , HOH B:681binding site for residue SO4 B 502
12AD3SOFTWAREHIS B:336 , TRP B:340 , SER B:351 , HIS B:352 , CYS B:354 , ASN B:356 , HOH B:608binding site for residue SO4 B 503
13AD4SOFTWAREARG B:104 , SER B:106 , ARG B:111binding site for residue SO4 B 504
14AD5SOFTWAREARG B:123 , THR B:142 , SER B:358 , PRO B:359 , SER B:360binding site for residue SO4 B 505
15AD6SOFTWAREASN B:205 , HOH B:611 , HOH B:681binding site for residue SO4 B 506
16AD7SOFTWARELYS B:189binding site for residue SO4 B 507
17AD8SOFTWAREGLU B:176 , ARG B:206binding site for residue GOL B 508
18AD9SOFTWAREGLU B:271 , VAL B:272binding site for residue GOL B 509

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5D7H)

(-) 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 5D7H)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5D7H)

(-) Exons   (0, 0)

(no "Exon" information available for 5D7H)

(-) 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..eeeeeeeee.......eee.....eeee........eeeeeeeeee..eeeeeeeeee.....eee.eeee.....ee.....eeeee.....hhhhhhhheeeeee....eeeee....eeeeee........eeeeeee....eee..eee..eeeeeeee...eeeeee....eeeeee..eeeeeee............eeee...eeeeeeee.hhhh.........eeeeeeeee......eeee.hhhh............eeehhhhhhhhhhhh....eeeee.............hhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5d7h A  58 LVPKLTASVTDGAVGVTVDAPVSVTAADGVLAAVTMVNENGRPVAGRLSPDGLRWSTTEQLGYNRRYTLNATALGLGGAATRQLTFQTSSPAHLTMPYVMPGDGEVVGVGEPVAIRFDENIADRGAAEKAIKITTNPPVEGAFYWLNNREVRWRPEHFWKPGTAVDVAVNTYGVDLGEGMFGEDNVQTHFTIGDEVIATADDNTKILTVRVNGEVVKSMPTSMGKDSTPTANGIYIVGSRYKHIIMDSSTYGVPVNSPNGYRTDVDWATQISYSGVFVHSAPWSVGAQGHTNTSHGCLNVSPSNAQWFYDHVKRGDIVEVVNTVGGTLPGIDGLGDWNIPWDQWRAGNAK 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:352
                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeee...............eeeee..eeeeeeeee.......eee.....eeee........eeeeeeeeee..eeeeeeeeee.....eee.eeee....eee.....eeeee.....hhhhhhhheeeeee....eeeee....eeeeee........eeeeeee.........eee..eeeeeeee...eeeeee....eeeeee..eeeeeeeee..........eeee...eeeeeeee.hhhh.........eeeeeeeee......eeee.hhhh............eeehhhhhhhhhhhh....eeeee.............hhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5d7h B  56 DLLVPKLTASVTDGAVGVTVDAPVSVTAADGVLAAVTMVNENGRPVAGRLSPDGLRWSTTEQLGYNRRYTLNATALGLGGAATRQLTFQTSSPAHLTMPYVMPGDGEVVGVGEPVAIRFDENIADRGAAEKAIKITTNPPVEGAFYWLNNREVRWRPEHFWKPGTAVDVAVNTYGVDLGEGMFGEDNVQTHFTIGDEVIATADDNTKILTVRVNGEVVKSMPTSMGKDSTPTANGIYIVGSRYKHIIMDSSTYGVPVNSPNGYRTDVDWATQISYSGVFVHSAPWSVGAQGHTNTSHGCLNVSPSNAQWFYDHVKRGDIVEVVNTVGGTLPGIDGLGDWNIPWDQWRAGNAK 407
                                    65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405
   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 5D7H)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5D7H)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5D7H)

(-) Gene Ontology  (14, 22)

Asymmetric Unit(hide GO term definitions)

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  5d7h
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 Related Entries

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        LDT2_MYCTO | O53223: 3tur 3tx4 3u1p 3u1q 3vae 3vyn 3vyo 3vyp 4gsq 4gsr 4gsu 4hu2 4huc 5dc2 5dcc 5du7 5duj 5lbg
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