Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF LIPDF
 
Authors :  Z. Zhou, X. Song, Y. Li, W. Gong
Date :  06 Dec 04  (Deposition) - 21 Dec 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A,B  (2x)
Keywords :  Open And Close Conformation, Pdf, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Z. Zhou, X. Song, Y. Li, W. Gong
Unique Structural Characteristics Of Peptide Deformylase From Pathogenic Bacterium Leptospira Interrogans
J. Mol. Biol. V. 339 207 2004
PubMed-ID: 15123432  |  Reference-DOI: 10.1016/J.JMB.2004.03.045
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PEPTIDE DEFORMYLASE
    Chains: A, B
    EC Number: 3.5.1.88
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET22B(+)
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: DEF
    Organism Scientific: LEPTOSPIRA INTERROGANS
    Organism Taxid: 173
    Synonym: LIPDF, PDF, POLYPEPTIDE DEFORMYLASE

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 11)

Asymmetric Unit (3, 11)
No.NameCountTypeFull Name
1FMT8Ligand/IonFORMIC ACID
2GLY1Mod. Amino AcidGLYCINE
3ZN2Ligand/IonZINC ION
Biological Unit 1 (2, 9)
No.NameCountTypeFull Name
1FMT8Ligand/IonFORMIC ACID
2GLY1Mod. Amino AcidGLYCINE
3ZN-1Ligand/IonZINC ION
Biological Unit 2 (2, 18)
No.NameCountTypeFull Name
1FMT16Ligand/IonFORMIC ACID
2GLY2Mod. Amino AcidGLYCINE
3ZN-1Ligand/IonZINC ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLN A:53 , CYS A:101 , HIS A:143 , HIS A:147 , FMT A:723BINDING SITE FOR RESIDUE ZN A 513
02AC2SOFTWAREGLN B:53 , CYS B:101 , HIS B:143 , HIS B:147 , FMT B:716BINDING SITE FOR RESIDUE ZN B 513
03AC3SOFTWAREVAL B:47 , TYR B:71 , PHE B:97 , GLU B:99 , GLY B:100 , TYR B:136 , HIS B:143 , GLU B:144 , FMT B:717BINDING SITE FOR RESIDUE GLY B 1001
04AC4SOFTWAREGLY B:48 , GLN B:53 , CYS B:101 , LEU B:102 , HIS B:143 , GLU B:144 , HIS B:147 , ZN B:513 , FMT B:717BINDING SITE FOR RESIDUE FMT B 716
05AC5SOFTWAREGLY B:46 , VAL B:47 , ARG B:70 , TYR B:71 , GLY B:100 , CYS B:101 , LEU B:102 , FMT B:716 , GLY B:1001 , HOH B:1012BINDING SITE FOR RESIDUE FMT B 717
06AC6SOFTWAREARG A:80 , LYS A:137 , TYR A:141BINDING SITE FOR RESIDUE FMT A 718
07AC7SOFTWAREGLY A:106 , PHE A:165 , ASN A:166 , GLU A:167 , HOH A:781 , ARG B:7BINDING SITE FOR RESIDUE FMT A 719
08AC8SOFTWAREASN B:84 , VAL B:86 , TRP B:121 , GLN B:128BINDING SITE FOR RESIDUE FMT B 720
09AC9SOFTWAREGLU B:79 , ARG B:80 , HIS B:173 , HOH B:1027 , HOH B:1077 , HOH B:1078 , HOH B:1090 , HOH B:1152BINDING SITE FOR RESIDUE FMT B 721
10BC1SOFTWAREPRO A:11 , LYS A:15 , ARG B:42 , HIS B:173 , ASN B:174 , VAL B:175 , HOH B:1122BINDING SITE FOR RESIDUE FMT B 722
11BC2SOFTWAREGLY A:48 , GLN A:53 , CYS A:101 , LEU A:102 , GLU A:144 , ZN A:513BINDING SITE FOR RESIDUE FMT A 723

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1Y6H)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1Y6H)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1Y6H)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1Y6H)

(-) Exons   (0, 0)

(no "Exon" information available for 1Y6H)

(-) 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:177
 aligned with DEF_LEPIN | Q93LE9 from UniProtKB/Swiss-Prot  Length:178

    Alignment length:177
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       
            DEF_LEPIN     2 SVRKILRMGDPILRKISEPVTEDEIQTKEFKKLIRDMFDTMRHAEGVGLAAPQIGILKQIVVVGSEDNERYPGTPDVPERIILNPVITPLTKDTSGFWEGCLSVPGMRGYVERPNQIRMQWMDEKGNQFDETIDGYKAIVYQHECDHLQGILYVDRLKDTKLFGFNETLDSSHNVLD 178
               SCOP domains d1y6ha_ A: Peptide deformylase                                                                                                                                                    SCOP domains
               CATH domains 1y6hA00 A:1-177 Peptide Deformylase                                                                                                                                               CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhh.....hhhhh.hhhhhhhhhhhhhhhhhh...eee.hhhh....eeee................eeeeeeeeee....eeeeeeee..eeeeeeeeeee.eeeeeee.....eeeeeeehhhhhhhhhhhhhhh..hhhhhh.....eeehhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1y6h A   1 SVRKILRMGDPILRKISEPVTEDEIQTKEFKKLIRDMFDTMRHAEGVGLAAPQIGILKQIVVVGSEDNERYPGTPDVPERIILNPVITPLTKDTSGFWEGCLSVPGMRGYVERPNQIRMQWMDEKGNQFDETIDGYKAIVYQHECDHLQGILYVDRLKDTKLFGFNETLDSSHNVLD 177
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       


Chain B from PDB  Type:PROTEIN  Length:177
 aligned with DEF_LEPIN | Q93LE9 from UniProtKB/Swiss-Prot  Length:178

    Alignment length:177
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       
            DEF_LEPIN     2 SVRKILRMGDPILRKISEPVTEDEIQTKEFKKLIRDMFDTMRHAEGVGLAAPQIGILKQIVVVGSEDNERYPGTPDVPERIILNPVITPLTKDTSGFWEGCLSVPGMRGYVERPNQIRMQWMDEKGNQFDETIDGYKAIVYQHECDHLQGILYVDRLKDTKLFGFNETLDSSHNVLD 178
               SCOP domains d1y6hb_ B: Peptide deformylase                                                                                                                                                    SCOP domains
               CATH domains 1y6hB00 B:1-177 Peptide Deformylase                                                                                                                                               CATH domains
           Pfam domains (1) -Pep_deformylase-1y6hB01 B:2-163                                                                                                                                   -------------- Pfam domains (1)
           Pfam domains (2) -Pep_deformylase-1y6hB02 B:2-163                                                                                                                                   -------------- Pfam domains (2)
         Sec.struct. author .........hhhhhh.......hhhhhhhhhhhhhhhhhhhhhh...eee.hhhh....eeeeee...........eeeeeeeeeeeee....eeeeeeee..eeeeeeeeeee.eeeeeee.....eeeeeeehhhhhhhhhhhhhhh..hhhhhh.....eeehhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1y6h B   1 SVRKILRMGDPILRKISEPVTEDEIQTKEFKKLIRDMFDTMRHAEGVGLAAPQIGILKQIVVVGSEDNERYPGTPDVPERIILNPVITPLTKDTSGFWEGCLSVPGMRGYVERPNQIRMQWMDEKGNQFDETIDGYKAIVYQHECDHLQGILYVDRLKDTKLFGFNETLDSSHNVLD 177
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170
   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  (1, 2)

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

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 2)

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

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (DEF_LEPIN | Q93LE9)
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.

 Visualization

(-) Interactive Views

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
    FMT  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GLY  [ 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 ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    BC1  [ RasMol ]  +environment [ RasMol ]
    BC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1y6h)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

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 ](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)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1y6h
    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_LEPIN | Q93LE9
    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

(-) Analysis Tools

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_LEPIN | Q93LE9
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        DEF_LEPIN | Q93LE9: 1sv2 1szz 1vev 1vey 1vez

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1Y6H)