1LRU - JenaLib

Asym.Unit - manually (Jmol Viewer)

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF E.COLI PEPTIDE DEFORMYLASE COMPLEXED WITH ANTIBIOTIC ACTINONIN

Authors :   J. -P. Guilloteau, M. Mathieu, C. Giglione, V. Blanc, A. Dupuy, M. Chevrier, P. Gil, A. Famechon, T. Meinnel, V. Mikol

Date :   16 May 02 (Deposition) - 24 Jul 02 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

Chains :   Asym. Unit : A,B,C
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: C  (1x)
Biol. Unit 4: B (1x),C (1x)

Keywords :   Actinonin, Inhibition, Polypeptide Deformylase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. P. Guilloteau, M. Mathieu, C. Giglione, V. Blanc, A. Dupuy, M. Chevrier, P. Gil, A. Famechon, T. Meinnel, V. Mikol
The Crystal Structures Of Four Peptide Deformylases Bound To The Antibiotic Actinonin Reveal Two Distinct Types: A Platform For The Structure-Based Design Of Antibacterial Agents.
J. Mol. Biol. V. 320 951 2002
PubMed-ID: 12126617 | Reference-DOI: 10.1016/S0022-2836(02)00549-1
(for further references see the PDB file header)

Molecule 1 - PEPTIDE DEFORMYLASE
	Chains	:	A, B, C
	EC Number	:	3.5.1.88
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	PDF, POLYPEPTIDE DEFORMYLASE

		1	2	3
Asymmetric Unit	:	A	B	C
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (1x)	:			C
Biological Unit 4 (1x)	:		B (1x)	C (1x)

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 8)

No.	Name	Count	Type	Full Name
1	BB2	3	Ligand/Ion	ACTINONIN
2	SO4	2	Ligand/Ion	SULFATE ION
3	ZN	3	Ligand/Ion	ZINC ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	BB2	1	Ligand/Ion	ACTINONIN
2	SO4	-1	Ligand/Ion	SULFATE ION
3	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (2, 3)

No.	Name	Count	Type	Full Name
1	BB2	1	Ligand/Ion	ACTINONIN
2	SO4	2	Ligand/Ion	SULFATE ION
3	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 3 (1, 1)

No.	Name	Count	Type	Full Name
1	BB2	1	Ligand/Ion	ACTINONIN
2	SO4	-1	Ligand/Ion	SULFATE ION
3	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 4 (2, 3)

No.	Name	Count	Type	Full Name
1	BB2	1	Ligand/Ion	ACTINONIN
2	SO4	2	Ligand/Ion	SULFATE ION
3	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CYS A:90 , HIS A:132 , HIS A:136 , BB2 A:501	BINDING SITE FOR RESIDUE ZN A 601
2	AC2	SOFTWARE	GLN B:50 , CYS B:90 , HIS B:132 , HIS B:136 , BB2 B:502	BINDING SITE FOR RESIDUE ZN B 602
3	AC3	SOFTWARE	GLN C:50 , CYS C:90 , HIS C:132 , HIS C:136 , BB2 C:503	BINDING SITE FOR RESIDUE ZN C 603
4	AC4	SOFTWARE	HIS B:54 , GLN B:55 , ARG C:29	BINDING SITE FOR RESIDUE SO4 B 701
5	AC5	SOFTWARE	ARG B:29 , HIS C:54 , GLN C:55 , HOH C:746	BINDING SITE FOR RESIDUE SO4 B 702
6	AC6	SOFTWARE	GLY A:43 , ILE A:44 , GLY A:45 , GLN A:50 , GLU A:87 , GLY A:89 , CYS A:90 , LEU A:91 , ARG A:97 , LEU A:125 , HIS A:132 , GLU A:133 , HIS A:136 , ZN A:601 , HOH A:684	BINDING SITE FOR RESIDUE BB2 A 501
7	AC7	SOFTWARE	GLY B:43 , ILE B:44 , GLY B:45 , GLN B:50 , GLU B:87 , GLU B:88 , GLY B:89 , CYS B:90 , LEU B:91 , ARG B:97 , CYS B:129 , HIS B:132 , GLU B:133 , HIS B:136 , ZN B:602	BINDING SITE FOR RESIDUE BB2 B 502
8	AC8	SOFTWARE	GLY C:43 , ILE C:44 , GLY C:45 , GLN C:50 , GLU C:87 , GLU C:88 , GLY C:89 , CYS C:90 , LEU C:91 , ARG C:97 , HIS C:132 , GLU C:133 , HIS C:136 , ZN C:603	BINDING SITE FOR RESIDUE BB2 C 503

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

Asymmetric Unit

No.	Residues
1	Ile A:8	-	Pro A:9
2	Ile B:8	-	Pro B:9
3	Ile C:8	-	Pro C:9

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

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

(no "Exon" information available for 1LRU)

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:164
 aligned with DEF_ECOLI | P0A6K3 from UniProtKB/Swiss-Prot  Length:169

    Alignment length:164
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161    
            DEF_ECOLI     2 SVLQVLHIPDERLRKVAKPVEEVNAEIQRIVDDMFETMYAEEGIGLAATQVDIHQRIIVIDVSENRDERLVLINPELLEKSGETGIEEGCLSIPEQRALVPRAEKVKIRALDRDGKPFELEADGLLAICIQHEMDHLVGKLFMDYLSPLKQQRIRQKVEKLDRL 165
               SCOP domains d1lrua_ A: Peptide deformylase                                                                                                                                       SCOP domains
               CATH domains 1lruA00 A:1-164 Peptide Deformylase                                                                                                                                  CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhh........hhhhhhhhhhhhhhhhhh...eee.hhhh....eeeee.......eeeeeeeeeeeee.....eee.......eee.....eeeeeee.....eeeeeehhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1lru A   1 SVLQVLHIPDERLRKVAKPVEEVNAEIQRIVDDMFETMYAEEGIGLAATQVDIHQRIIVIDVSENRDERLVLINPELLEKSGETGIEEGCLSIPEQRALVPRAEKVKIRALDRDGKPFELEADGLLAICIQHEMDHLVGKLFMDYLSPLKQQRIRQKVEKLDRL 164
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160

Chain B from PDB  Type:PROTEIN  Length:164
 aligned with DEF_ECOLI | P0A6K3 from UniProtKB/Swiss-Prot  Length:169

    Alignment length:164
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161    
            DEF_ECOLI     2 SVLQVLHIPDERLRKVAKPVEEVNAEIQRIVDDMFETMYAEEGIGLAATQVDIHQRIIVIDVSENRDERLVLINPELLEKSGETGIEEGCLSIPEQRALVPRAEKVKIRALDRDGKPFELEADGLLAICIQHEMDHLVGKLFMDYLSPLKQQRIRQKVEKLDRL 165
               SCOP domains d1lrub_ B: Peptide deformylase                                                                                                                                       SCOP domains
               CATH domains 1lruB00 B:1-164 Peptide Deformylase                                                                                                                                  CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhh........hhhhhhhhhhhhhhhhhhh..eee.hhhh....eeee.........eeeeeeeeeeee.....eee.......eee.....eeeeeee.....eeeeeehhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1lru B   1 SVLQVLHIPDERLRKVAKPVEEVNAEIQRIVDDMFETMYAEEGIGLAATQVDIHQRIIVIDVSENRDERLVLINPELLEKSGETGIEEGCLSIPEQRALVPRAEKVKIRALDRDGKPFELEADGLLAICIQHEMDHLVGKLFMDYLSPLKQQRIRQKVEKLDRL 164
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160

Chain C from PDB  Type:PROTEIN  Length:161
 aligned with DEF_ECOLI | P0A6K3 from UniProtKB/Swiss-Prot  Length:169

    Alignment length:161
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161 
            DEF_ECOLI     2 SVLQVLHIPDERLRKVAKPVEEVNAEIQRIVDDMFETMYAEEGIGLAATQVDIHQRIIVIDVSENRDERLVLINPELLEKSGETGIEEGCLSIPEQRALVPRAEKVKIRALDRDGKPFELEADGLLAICIQHEMDHLVGKLFMDYLSPLKQQRIRQKVEKL 162
               SCOP domains d1lruc_ C: Peptide deformylase                                                                                                                                    SCOP domains
               CATH domains 1lruC00 C:1-161 Peptide Deformylase                                                                                                                               CATH domains
           Pfam domains (1) -Pep_deformylase-1lruC01 C:2-152                                                                                                                        --------- Pfam domains (1)
           Pfam domains (2) -Pep_deformylase-1lruC02 C:2-152                                                                                                                        --------- Pfam domains (2)
           Pfam domains (3) -Pep_deformylase-1lruC03 C:2-152                                                                                                                        --------- Pfam domains (3)
         Sec.struct. author .........hhhhhh........hhhhhhhhhhhhhhhhhh...eee.hhhh....eeee.........eeeeeeeeeeee..eeeeeee..eeeeeeeeee..eeeeeee.....eeeeeehhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1lru C   1 SVLQVLHIPDERLRKVAKPVEEVNAEIQRIVDDMFETMYAEEGIGLAATQVDIHQRIIVIDVSENRDERLVLINPELLEKSGETGIEEGCLSIPEQRALVPRAEKVKIRALDRDGKPFELEADGLLAICIQHEMDHLVGKLFMDYLSPLKQQRIRQKVEKL 161
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160

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(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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)

Escherichia coli [TaxId: 562] (21)

1a	d1lrua_	A:
1b	d1lrub_	B:
1c	d1lruc_	C:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Alpha-Beta Complex (3881)

Topology: Peptide Deformylase (68)

Homologous Superfamily: Peptide Deformylase (68)

Escherichia coli. Organism_taxid: 562. (2)

1a	1lruA00	A:1-164
1b	1lruB00	B:1-164
1c	1lruC00	C:1-161

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

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

Family: Pep_deformylase (48)

Escherichia coli (strain K12) (8)

1a	Pep_deformylase-1lruC01	C:2-152
1b	Pep_deformylase-1lruC02	C:2-152
1c	Pep_deformylase-1lruC03	C:2-152

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (DEF_ECOLI | P0A6K3)

molecular function
	GO:0008198	ferrous iron binding	Interacting selectively and non-covalently with ferrous iron, Fe(II).
	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.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0043022	ribosome binding	Interacting selectively and non-covalently with any part of a ribosome.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
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.
cellular component
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

Asymmetric Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		BB2	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		SO4	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		ZN	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]
		AC6	[ RasMol ]	+environment [ RasMol ]
		AC7	[ RasMol ]	+environment [ RasMol ]
		AC8	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Ile A:8 - Pro A:9	[ RasMol ]
		Ile B:8 - Pro B:9	[ RasMol ]
		Ile C:8 - Pro C:9	[ RasMol ]

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]
		Biological Unit 3	[ Jena3D ]
		Biological Unit 4	[ Jena3D ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Asym. Unit - sites PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 1 - sites PNG format \| Biol. Unit 2 PNG format \| Biol. Unit 3 PNG format \| Biol. Unit 4 PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	1lru
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	DEF_ECOLI \| P0A6K3
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	3.5.1.88
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	DEF_ECOLI \| P0A6K3
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

1lqw	1LQW IS THE CRYSTAL STRUCTURE OF S.AUREUS DEFORMYLASE.
1lqy	1LQY IS THE CRYSTAL STRUCTURE OF B.STEAROTHERMOPHILUS DEFORMYLASE.
1lry	1LRY IS THE CRYSTAL STRUCTURE OF P.AERUGINOSA DEFORMYLASE.

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 8)

Sites (8, 8)

SS Bonds (0, 0)

Cis Peptide Bonds (3, 3)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 3)

CATH Domains (1, 3)

Pfam Domains (1, 3)

Gene Ontology (12, 12)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File