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(-) Description

Title :  X-RAY CRYSTAL STRUCTURE OF A TEBIPENEM ADDUCT OF L,D TRANSPEPTIDASE 2 FROM MYCOBACTERIUM TUBERCULOSIS
 
Authors :  Y. Pan, L. Basta, G. Lamichhane, M. A. Bianchet
Date :  23 Aug 15  (Deposition) - 28 Sep 16  (Release) - 28 Sep 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.45
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  L, D -Transpeptidase, Carbapenems Tebipenem-Adduct, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Pan, L. A. Basta, H. Saavedra, R. Mattoo, K. Pankaj, E. P. Lloyd, 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
(for further references see the PDB file header)

(-) 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
    Fragment: UNP RESIDUES 56-408
    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  (6, 33)

Asymmetric Unit (6, 33)
No.NameCountTypeFull Name
158U2Ligand/Ion(4S)-4-METHYL-2,5,7-TRIOXOHEPTANOIC ACID
2EDO2Ligand/Ion1,2-ETHANEDIOL
3GOL4Ligand/IonGLYCEROL
4PEG9Ligand/IonDI(HYDROXYETHYL)ETHER
5PGE7Ligand/IonTRIETHYLENE GLYCOL
6SO49Ligand/IonSULFATE ION
Biological Unit 1 (6, 16)
No.NameCountTypeFull Name
158U1Ligand/Ion(4S)-4-METHYL-2,5,7-TRIOXOHEPTANOIC ACID
2EDO1Ligand/Ion1,2-ETHANEDIOL
3GOL2Ligand/IonGLYCEROL
4PEG3Ligand/IonDI(HYDROXYETHYL)ETHER
5PGE4Ligand/IonTRIETHYLENE GLYCOL
6SO45Ligand/IonSULFATE ION
Biological Unit 2 (6, 17)
No.NameCountTypeFull Name
158U1Ligand/Ion(4S)-4-METHYL-2,5,7-TRIOXOHEPTANOIC ACID
2EDO1Ligand/Ion1,2-ETHANEDIOL
3GOL2Ligand/IonGLYCEROL
4PEG6Ligand/IonDI(HYDROXYETHYL)ETHER
5PGE3Ligand/IonTRIETHYLENE GLYCOL
6SO44Ligand/IonSULFATE ION

(-) Sites  (33, 33)

Asymmetric Unit (33, 33)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREMET A:303 , TYR A:318 , GLY A:332 , HIS A:336 , TRP A:340 , SER A:351 , HIS A:352 , GLY A:353 , CYS A:354 , ASN A:356 , EDO A:516 , HOH A:604 , HOH A:715binding site for residue 58U A 501
02AC2SOFTWAREARG A:99 , ARG A:122 , SO4 A:506 , HOH A:641 , PRO B:311 , VAL B:312 , ASN B:313 , HOH B:649binding site for residue SO4 A 502
03AC3SOFTWAREGLU A:162 , ARG A:371 , HOH A:611 , HOH A:621binding site for residue SO4 A 503
04AC4SOFTWAREMET A:157 , ARG A:209 , TYR A:330 , ARG A:371 , HOH A:728binding site for residue SO4 A 504
05AC5SOFTWAREARG A:104 , SER A:106 , PRO A:107 , ARG A:111 , HOH A:605 , HOH A:713binding site for residue SO4 A 505
06AC6SOFTWAREASN A:95 , ARG A:99 , ARG A:122 , SO4 A:502 , SER B:306 , PRO B:311binding site for residue SO4 A 506
07AC7SOFTWAREASN A:204 , ASN A:205 , HOH A:607binding site for residue PEG A 507
08AC8SOFTWAREGLU A:185 , ALA A:199 , PHE A:200 , TRP A:401 , ARG A:402 , GLY A:404 , PEG A:509 , HOH A:654 , HOH A:690binding site for residue PEG A 508
09AC9SOFTWAREILE A:188 , ILE A:190 , GLY A:198 , TRP A:210 , PEG A:508 , PGE A:511 , HOH A:734binding site for residue PEG A 509
10AD1SOFTWAREHIS A:214 , PHE A:215 , LYS B:186binding site for residue PGE A 510
11AD2SOFTWARELYS A:189 , ILE A:190 , THR A:192 , VAL A:196 , TRP A:210 , PEG A:509 , HOH A:657binding site for residue PGE A 511
12AD3SOFTWAREVAL A:91 , THR A:92 , MET A:93 , VAL A:101 , GLY A:103 , TRP A:112binding site for residue PGE A 512
13AD4SOFTWARETHR A:256 , ASP A:258 , THR A:261 , ILE A:263 , THR A:265 , HOH A:606 , HOH A:618 , VAL B:196 , GLU B:197 , GLY B:198 , TRP B:210 , PEG B:506binding site for residue PGE A 513
14AD5SOFTWAREARG A:181 , TRP A:202 , LEU A:203 , ASN A:205 , ASN A:405 , HOH A:607binding site for residue GOL A 514
15AD6SOFTWAREVAL A:75 , ASP A:76 , ALA A:77 , PRO A:78 , GLN A:117 , LEU A:118binding site for residue GOL A 515
16AD7SOFTWARETYR A:318 , SER A:331 , 58U A:501 , HOH A:691binding site for residue EDO A 516
17AD8SOFTWAREARG B:297 , ARG B:371 , PEG B:510 , HOH B:604 , HOH B:643binding site for residue SO4 B 502
18AD9SOFTWAREPRO A:311 , VAL A:312 , ASN A:313 , ARG B:122 , SO4 B:504binding site for residue SO4 B 503
19AE1SOFTWARESER A:306 , PRO A:311 , ASN B:95 , ASN B:97 , ARG B:99 , ARG B:122 , SO4 B:503binding site for residue SO4 B 504
20AE2SOFTWAREARG B:104 , PRO B:107 , ARG B:111 , HOH B:714binding site for residue SO4 B 505
21AE3SOFTWAREPGE A:513 , ILE B:188 , LYS B:189 , ILE B:190binding site for residue PEG B 506
22AE4SOFTWAREVAL A:71 , HIS B:214 , HOH B:605binding site for residue PEG B 507
23AE5SOFTWARELEU B:385 , GLY B:387 , ILE B:396 , PGE B:514 , HOH B:733binding site for residue PEG B 508
24AE6SOFTWAREASP B:251 , HIS B:368binding site for residue PEG B 509
25AE7SOFTWAREMET B:157 , PRO B:158 , GLY B:159 , GLU B:162 , VAL B:164 , ARG B:371 , SO4 B:502binding site for residue PEG B 510
26AE8SOFTWAREALA B:183 , LYS B:186 , ALA B:187 , VAL B:231 , ASP B:232binding site for residue PEG B 511
27AE9SOFTWAREGLU B:376 , TRP B:394 , ASN B:395 , HOH B:621binding site for residue PGE B 512
28AF1SOFTWAREGLU B:168 , PRO B:169 , GLY B:295 , SER B:296 , GLN B:327 , TYR B:330 , ARG B:371binding site for residue PGE B 513
29AF2SOFTWAREARG B:181 , TYR B:201 , TRP B:202 , LEU B:203 , ILE B:388 , ASN B:405 , PEG B:508 , HOH B:642 , HOH B:688 , HOH B:699binding site for residue PGE B 514
30AF3SOFTWAREGLU B:213 , HIS B:214 , PHE B:215 , ILE B:291 , TRP B:394binding site for residue GOL B 515
31AF4SOFTWAREALA B:90 , VAL B:91 , LEU B:105binding site for residue GOL B 516
32AF5SOFTWARETYR B:318 , SER B:331 , GLY B:353 , 58U B:501binding site for residue EDO B 517
33AF6SOFTWARESER B:279 , MET B:280 , 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 , EDO B:517 , HOH B:697binding site for Di-peptide 58U B 501 and CYS B 354

(-) SS Bonds  (0, 0)

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

(-) 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 5DCC)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5DCC)

(-) 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:352
                                                                                                                                                                                                                                                                                                                                                                                                
               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
                 5dcc A  56 DLLVPKLTASVTDGAVGVTVDAPVSVTAADGVLAAVTMVNDNGRPVAGRLSPDGLRWSTTEQLGYNRRYTLNATALGLGGAATRQLTFQTSSPAHLTMPYVMPGDGEVVGVGEPVAIRFDENIADRGAAEKAIKITTNPPVEGAFYWLNNREVRWRPEHFWKPGTAVDVAVNTYGVDLGEGMFGEDNVQTHFTIGDEVIATADDNTKILTVRVNGEVVKSMPTSMGKDSTPTANGIYIVGSRYKHIIMDSSTYGVPVNSPNGYRTDVDWATQISYSGVFVHSAPWSVGAQGHTNTSHGCLNVSPSNAQWFYDHVKRGDIVEVVNTVGGTLPGIDGLGDWNIPWDQWRAGNAK 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  


Chain B from PDB  Type:PROTEIN  Length:353
                                                                                                                                                                                                                                                                                                                                                                                                 
               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
                 5dcc B  56 DLLVPKLTASVTDGAVGVTVDAPVSVTAADGVLAAVTMVNDNGRPVAGRLSPDGLRWSTTEQLGYNRRYTLNATALGLGGAATRQLTFQTSSPAHLTMPYVMPGDGEVVGVGEPVAIRFDENIADRGAAEKAIKITTNPPVEGAFYWLNNREVRWRPEHFWKPGTAVDVAVNTYGVDLGEGMFGEDNVQTHFTIGDEVIATADDNTKILTVRVNGEVVKSMPTSMGKDSTPTANGIYIVGSRYKHIIMDSSTYGVPVNSPNGYRTDVDWATQISYSGVFVHSAPWSVGAQGHTNTSHGCLNVSPSNAQWFYDHVKRGDIVEVVNTVGGTLPGIDGLGDWNIPWDQWRAGNAKA 408
                                    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 5DCC)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (14, 22)

Asymmetric Unit(hide GO term definitions)

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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 4gsu 4hu2 4huc 5d7h 5dc2 5du7 5duj 5lbg
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(-) Related Entries Specified in the PDB File

3tur APO(3,3)-L,D-TRANSPEPTIDASE 2 OF MYCOBACTERIIUM TUBERCULOSIS IN COMPLEX ITH PETIDOGLYCAN FRAGMENT
5dc2
5dh7 BIAPENEM-ADDUCT OF (3,3) L,D-TRANSPEPTIDASE 2