5DUJ - JenaLib

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Biological Unit 3 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF LDTMT2 IN COMPLEX WITH FAROPENEM ADDUCT

Authors :   P. Kumar, G. Lamichhane

Date :   18 Sep 15 (Deposition) - 28 Sep 16 (Release) - 28 Dec 16 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.17

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: A (1x),B (1x)

Keywords :   Ld-Transpeptidase, Peptidoglycan Synthesis Enzyme, Cell Wall Enzyme, Transferase (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

Molecule 1 - L,D-TRANSPEPTIDASE 2
	Chains	:	A, B
	EC Number	:	2.3.2.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28A
	Expression System Strain	:	BL21 (DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 42-408
	Gene	:	LDTB, MT2594, V735_02606
	Organism Scientific	:	MYCOBACTERIUM TUBERCULOSIS
	Organism Taxid	:	83331
	Strain	:	CDC 1551 / OSHKOSH
	Synonym	:	LDT 2,LDT(MT2)

		1	2
Asymmetric Unit	:	A	B
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)

Asymmetric Unit (3, 5)

No.	Name	Count	Type	Full Name
1	BME	2	Ligand/Ion	BETA-MERCAPTOETHANOL
2	DGF	2	Ligand/Ion	(2R,5R)-2-[(2S,3R)-3-HYDROXY-1-OXOBUTAN-2-YL]-5-[(2R)-TETRAHYDROFURAN-2-YL]-2,5-DIHYDRO-1,3-THIAZOLE-4-CARBOXYLIC ACID
3	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 1 (3, 3)

No.	Name	Count	Type	Full Name
1	BME	1	Ligand/Ion	BETA-MERCAPTOETHANOL
2	DGF	1	Ligand/Ion	(2R,5R)-2-[(2S,3R)-3-HYDROXY-1-OXOBUTAN-2-YL]-5-[(2R)-TETRAHYDROFURAN-2-YL]-2,5-DIHYDRO-1,3-THIAZOLE-4-CARBOXYLIC ACID
3	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	BME	1	Ligand/Ion	BETA-MERCAPTOETHANOL
2	DGF	1	Ligand/Ion	(2R,5R)-2-[(2S,3R)-3-HYDROXY-1-OXOBUTAN-2-YL]-5-[(2R)-TETRAHYDROFURAN-2-YL]-2,5-DIHYDRO-1,3-THIAZOLE-4-CARBOXYLIC ACID
3	SO4	-1	Ligand/Ion	SULFATE ION

Biological Unit 3 (3, 3)

No.	Name	Count	Type	Full Name
1	BME	1	Ligand/Ion	BETA-MERCAPTOETHANOL
2	DGF	1	Ligand/Ion	(2R,5R)-2-[(2S,3R)-3-HYDROXY-1-OXOBUTAN-2-YL]-5-[(2R)-TETRAHYDROFURAN-2-YL]-2,5-DIHYDRO-1,3-THIAZOLE-4-CARBOXYLIC ACID
3	SO4	1	Ligand/Ion	SULFATE ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:297 , ARG A:371 , HOH A:625 , HOH A:716 , HOH A:738	binding site for residue SO4 A 501
2	AC2	SOFTWARE	MET A:303 , TYR A:318 , HIS A:352 , CYS A:354 , DGF A:503	binding site for residue BME A 502
3	AC3	SOFTWARE	TYR A:318 , SER A:331 , GLY A:332 , HIS A:352 , GLY A:353 , CYS A:354 , BME A:502	binding site for residue DGF A 503
4	AC4	SOFTWARE	MET B:303 , HIS B:336 , SER B:351 , HIS B:352 , CYS B:354 , DGF B:502	binding site for residue BME B 501

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

Asymmetric Unit

No.	Residues
1	Met A:157	-	Pro A:158
2	Asn A:193	-	Pro A:194
3	Met B:157	-	Pro B:158
4	Asn B:193	-	Pro B:194
5	His B:352	-	Gly B:353

(no "SAP(SNP)/Variant" information available for 5DUJ)

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

(no "Exon" information available for 5DUJ)

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:351
                                                                                                                                                                                                                                                                                                                                                                                               
               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
                 5duj A  57 LLVPKLTASVTDGAVGVTVDAPVSVTAADGVLAAVTMVNDNGRPVAGRLSPDGLRWSTTEQLGYNRRYTLNATALGLGGAATRQLTFQTSSPAHLTMPYVMPGDGEVVGVGEPVAIRFDENIADRGAAEKAIKITTNPPVEGAFYWLNNREVRWRPEHFWKPGTAVDVAVNTYGVDLGEGMFGEDNVQTHFTIGDEVIATADDNTKILTVRVNGEVVKSMPTSMGKDSTPTANGIYIVGSRYKHIIMDSSTYGVPVNSPNGYRTDVDWATQISYSGVFVHSAPWSVGAQGHTNTSHGCLNVSPSNAQWFYDHVKRGDIVEVVNTVGGTLPGIDGLGDWNIPWDQWRAGNAK 407
                                    66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406

Chain B 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.....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
                 5duj B  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

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 '\|'

(no "SCOP Domain" information available for 5DUJ)

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

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

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	Cis Peptide Bonds
		Asn A:193 - Pro A:194	[ RasMol ]
		Asn B:193 - Pro B:194	[ RasMol ]
		His B:352 - Gly B:353	[ RasMol ]
		Met A:157 - Pro A:158	[ RasMol ]
		Met B:157 - Pro B:158	[ RasMol ]

Biological Units
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		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]
		Biological Unit 3	[ Jena3D ]

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Description

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