1S17 - JenaLib

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Title :   IDENTIFICATION OF NOVEL POTENT BICYCLIC PEPTIDE DEFORMYLASE INHIBITORS

Authors :   V. Molteni, X. He, J. Nabakka, K. Yang, A. Kreusch, P. Gordon, B. Bursula N. S. Ryder, R. Goldberg, Y. He

Date :   05 Jan 04 (Deposition) - 30 Mar 04 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.95

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

Keywords :   Peptide Deformylase Inhibitor, Rational Drug Design, Antibiotic, Protein-Ligand Complex, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   V. Molteni, X. He, J. Nabakka, K. Yang, A. Kreusch, P. Gordon, B. Bursulaya, I. Warner, T. Shin, T. Biorac, N. S. Ryder, R. Goldberg, J. Doughty, Y. He
Identification Of Novel Potent Bicyclic Peptide Deformylase Inhibitors
Bioorg. Med. Chem. Lett. V. 14 1477 2004
PubMed-ID: 15006385 | Reference-DOI: 10.1016/J.BMCL.2004.01.014
(for further references see the PDB file header)

Molecule 1 - PEPTIDE DEFORMYLASE
	Chains	:	A, B
	EC Number	:	3.5.1.88
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PMH4
	Expression System Strain	:	GENEHOGS
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	DEF, PA0019
	Organism Scientific	:	PSEUDOMONAS AERUGINOSA
	Organism Taxid	:	287
	Synonym	:	PDF, POLYPEPTIDE DEFORMYLASE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 5)

No.	Name	Count	Type	Full Name
1	GNR	2	Ligand/Ion	2-(3,4-DIHYDRO-3-OXO-2H-BENZO[B][1,4]THIAZIN-2-YL)-N-HYDROXYACETAMIDE
2	GOL	1	Ligand/Ion	GLYCEROL
3	NI	2	Ligand/Ion	NICKEL (II) ION

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	GNR	1	Ligand/Ion	2-(3,4-DIHYDRO-3-OXO-2H-BENZO[B][1,4]THIAZIN-2-YL)-N-HYDROXYACETAMIDE
2	GOL	1	Ligand/Ion	GLYCEROL
3	NI	-1	Ligand/Ion	NICKEL (II) ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	GNR	1	Ligand/Ion	2-(3,4-DIHYDRO-3-OXO-2H-BENZO[B][1,4]THIAZIN-2-YL)-N-HYDROXYACETAMIDE
2	GOL	-1	Ligand/Ion	GLYCEROL
3	NI	-1	Ligand/Ion	NICKEL (II) ION

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLN A:51 , CYS A:92 , HIS A:134 , HIS A:138 , GNR A:501	BINDING SITE FOR RESIDUE NI A 301
2	AC2	SOFTWARE	GLN B:51 , CYS B:92 , HIS B:134 , HIS B:138 , GNR B:601	BINDING SITE FOR RESIDUE NI B 302
3	AC3	SOFTWARE	GLY A:44 , ILE A:45 , GLY A:46 , GLN A:51 , TYR A:88 , GLU A:90 , GLY A:91 , CYS A:92 , LEU A:93 , HIS A:134 , GLU A:135 , HIS A:138 , NI A:301 , HOH A:584	BINDING SITE FOR RESIDUE GNR A 501
4	AC4	SOFTWARE	GLY B:44 , ILE B:45 , GLY B:46 , GLN B:51 , TYR B:88 , GLU B:90 , GLY B:91 , CYS B:92 , LEU B:93 , HIS B:134 , GLU B:135 , HIS B:138 , NI B:302	BINDING SITE FOR RESIDUE GNR B 601
5	AC5	SOFTWARE	ARG A:71 , VAL A:72 , ASP A:114 , ARG A:115 , PHE A:120 , HOH A:503	BINDING SITE FOR RESIDUE GOL A 401

(no "SS Bond" information available for 1S17)

Asymmetric Unit

No.	Residues
1	Phe A:9	-	Pro A:10
2	Ala A:42	-	Pro A:43
3	Phe B:9	-	Pro B:10
4	Ala B:42	-	Pro B:43

(no "SAP(SNP)/Variant" information available for 1S17)

(no "PROSITE Motif" information available for 1S17)

(no "Exon" information available for 1S17)

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
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Chain A from PDB  Type:PROTEIN  Length:166
 aligned with DEF_PSEAE | Q9I7A8 from UniProtKB/Swiss-Prot  Length:168

    Alignment length:166
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161      
            DEF_PSEAE     2 AILNILEFPDPRLRTIAKPVEVVDDAVRQLIDDMFETMYEAPGIGLAATQVNVHKRIVVMDLSEDKSEPRVFINPEFEPLTEDMDQYQEGCLSVPGFYENVDRPQKVRIKALDRDGNPFEEVAEGLLAVCIQHECDHLNGKLFVDYLSTLKRDRIRKKLEKQHRQQ 167
               SCOP domains d1s17a_ A: Peptide deformylase                                                                                                                                         SCOP domains
               CATH domains 1s17A00 A:2-167 Peptide Deformylase                                                                                                                                    CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhh........hhhhhhhhhhhhhhhhhh...eee.hhhh....eeeee.......eeeeeeeeeee....eeeeee.........eeeeee.eeeeeee.....eeeeeeehhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1s17 A   2 AILNILEFPDPRLRTIAKPVEVVDDAVRQLIDDMFETMYEAPGIGLAATQVNVHKRIVVMDLSEDKSEPRVFINPEFEPLTEEMDQYQEGCLSVPGFYENVDRPQKVRIKALDRDGNPFEEVAEGLLAVCIQHECDHLNGKLFVDYLSTLKRDRIRKKLEKQHRQQ 167
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161

Chain B from PDB  Type:PROTEIN  Length:164
 aligned with DEF_PSEAE | Q9I7A8 from UniProtKB/Swiss-Prot  Length:168

    Alignment length:164
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161    
            DEF_PSEAE     2 AILNILEFPDPRLRTIAKPVEVVDDAVRQLIDDMFETMYEAPGIGLAATQVNVHKRIVVMDLSEDKSEPRVFINPEFEPLTEDMDQYQEGCLSVPGFYENVDRPQKVRIKALDRDGNPFEEVAEGLLAVCIQHECDHLNGKLFVDYLSTLKRDRIRKKLEKQHR 165
               SCOP domains d1s17b_ B: Peptide deformylase                                                                                                                                       SCOP domains
               CATH domains 1s17B00 B:2-165 Peptide Deformylase                                                                                                                                  CATH domains
           Pfam domains (1) -Pep_deformylase-1s17B01 B:3-154                                                                                                                         ----------- Pfam domains (1)
           Pfam domains (2) -Pep_deformylase-1s17B02 B:3-154                                                                                                                         ----------- Pfam domains (2)
         Sec.struct. author .........hhhhhh........hhhhhhhhhhhhhhhhhh...eee.hhhh....eeeee.......eeeeeeeeeee....eeeeee.........eeeeee.eeeeeee.....eeeeeeehhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1s17 B   2 AILNILEFPDPRLRTIAKPVEVVDDAVRQLIDDMFETMYEAPGIGLAATQVNVHKRIVVMDLSEDKSEPRVFINPEFEPLTEEMDQYQEGCLSVPGFYENVDRPQKVRIKALDRDGNPFEEVAEGLLAVCIQHECDHLNGKLFVDYLSTLKRDRIRKKLEKQHR 165
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161

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 '\|'

Asymmetric Unit

Classes(

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Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

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Organisms( (-)

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Class: Alpha and beta proteins (a+b) (23004)

Fold: Peptide deformylase (87)

Superfamily: Peptide deformylase (87)

Family: Peptide deformylase (62)

Protein domain: Peptide deformylase (50)

Pseudomonas aeruginosa [TaxId: 287] (4)

1a	d1s17a_	A:
1b	d1s17b_	B:

Asymmetric Unit

Classes(

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Architectures( (-)

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Topologies( (-)

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Homologous Superfamilies( (-)

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Organisms( (-)

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Class: Alpha Beta (26913)

Architecture: Alpha-Beta Complex (3881)

Topology: Peptide Deformylase (68)

Homologous Superfamily: Peptide Deformylase (68)

Pseudomonas aeruginosa. Organism_taxid: 287. (1)

1a	1s17A00	A:2-167
1b	1s17B00	B:2-165

Asymmetric Unit

Clans(

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Families(

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Organisms( (-)

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Clan: no clan defined [family: Pep_deformylase] (48)

Family: Pep_deformylase (48)

Pseudomonas aeruginosa (3)

1a	Pep_deformylase-1s17B01	B:3-154
1b	Pep_deformylase-1s17B02	B:3-154

Asymmetric Unit(hide GO term definitions)

Chain A,B (DEF_PSEAE | Q9I7A8)

molecular function
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0005506	iron ion binding	Interacting selectively and non-covalently with iron (Fe) ions.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0042586	peptide deformylase activity	Catalysis of the reaction: formyl-L-methionyl peptide + H2O = formate + methionyl peptide.
biological process
	GO:0031365	N-terminal protein amino acid modification	The alteration of the N-terminal amino acid residue in a protein.
	GO:0043686	co-translational protein modification	The process of covalently altering one or more amino acids in a protein after translation has begun but before the protein has been released from the ribosome.
	GO:0006412	translation	The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome.

Asymmetric Unit
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	Cis Peptide Bonds
		Ala A:42 - Pro A:43	[ RasMol ]
		Ala B:42 - Pro B:43	[ RasMol ]
		Phe A:9 - Pro A:10	[ RasMol ]
		Phe B:9 - Pro B:10	[ RasMol ]

Biological Units
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Access by PDB/NDB ID
	1s17
		Family and Domain Information	:	ProDom \| SYSTERS
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	3.5.1.88
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	DEF_PSEAE \| Q9I7A8	:	1ix1 1lry 1n5n

1ix1	CRYSTAL STRUCTURE OF P. AERUGINOSA PEPTIDE DEFORMYLASE COMPLEXED WITH ANTIBIOTIC ACTINONIN
1n5n	CRYSTAL STRUCTURE OF PEPTIDE DEFORMYLASE FROM PSEUDOMONAS AERUGINOSA

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 5)

Sites (5, 5)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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