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

(-) Description

Title :  IODOPENTAFLUOROBENZENE BINDING IN THE HYDROPHOBIC CAVITY OF T4 LYSOZYME L99A MUTANT
 
Authors :  L. Liu, B. W. Matthews
Date :  01 Jul 08  (Deposition) - 11 Nov 08  (Release) - 09 Jun 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A
Keywords :  T4 Lysozyme, Halogen Bond, Hydrophobic Cavity, Halogenated Benzene, Antimicrobial, Bacteriolytic Enzyme, Glycosidase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Liu, W. A. Baase, B. W. Matthews
Halogenated Benzenes Bound Within A Non-Polar Cavity In T4 Lysozyme Provide Examples Of I. . . S And I. . . Se Halogen-Bonding.
J. Mol. Biol. V. 385 595 2009
PubMed-ID: 19014950  |  Reference-DOI: 10.1016/J.JMB.2008.10.086
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - LYSOZYME
    Chains: A
    EC Number: 3.2.1.17
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: E
    Mutation: YES
    Organism Scientific: BACTERIOPHAGE T4
    Organism Taxid: 10665
    Synonym: LYSIS PROTEIN, MURAMIDASE, ENDOLYSIN

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric/Biological Unit (3, 6)
No.NameCountTypeFull Name
1HED3Ligand/Ion2-HYDROXYETHYL DISULFIDE
2IBF1Ligand/Ion1,2,3,4,5-PENTAFLUORO-6-IODOBENZENE
3PO42Ligand/IonPHOSPHATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:14 , LYS A:19 , ARG A:125 , TRP A:126 , ASP A:127 , GLU A:128 , HOH A:908 , HOH A:1076 , HOH A:1110BINDING SITE FOR RESIDUE PO4 A 901
2AC2SOFTWAREGLN A:122 , ASN A:144 , ARG A:148 , HOH A:923 , HOH A:1083 , HOH A:1121 , HOH A:1127BINDING SITE FOR RESIDUE PO4 A 902
3AC3SOFTWAREILE A:78 , LEU A:84 , TYR A:88 , LEU A:91 , ALA A:99 , MET A:102 , LEU A:118 , LEU A:121 , PHE A:153BINDING SITE FOR RESIDUE IBF A 900
4AC4SOFTWAREASP A:72 , LEU A:79 , TYR A:88BINDING SITE FOR RESIDUE HED A 903
5AC5SOFTWAREASN A:68 , ASP A:72 , ALA A:93 , ILE A:100BINDING SITE FOR RESIDUE HED A 904
6AC6SOFTWAREGLY A:30 , HIS A:31 , LEU A:32 , ASP A:70 , PHE A:104 , HOH A:1040 , HOH A:1089 , HOH A:1138BINDING SITE FOR RESIDUE HED A 905

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3DN3)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3DN3)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3DN3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3DN3)

(-) Exons   (0, 0)

(no "Exon" information available for 3DN3)

(-) Sequences/Alignments

Asymmetric/Biological 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:162
 aligned with ENLYS_BPT4 | P00720 from UniProtKB/Swiss-Prot  Length:164

    Alignment length:162
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160  
           ENLYS_BPT4     1 MNIFEMLRIDERLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSELDKAIGRNCNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRCALINMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSIWYNQTPNRAKRVITTFRTGTWDAYK 162
               SCOP domains d3dn3a_ A: Phage T4 lysozyme                                                                                                                                       SCOP domains
               CATH domains 3dn3A00 A:1-162  [code=1.10.530.40, no name defined]                                                                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhh.eeeeee.....eeee..ee.....hhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3dn3 A   1 MNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSELDKAIGRNTNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRAAAINMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSRWYNQTPNRAKRVITTFRTGTWDAYK 162
                                    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 '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

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

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3DN3)

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (ENLYS_BPT4 | P00720)
molecular function
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    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:0016798    hydrolase activity, acting on glycosyl bonds    Catalysis of the hydrolysis of any glycosyl bond.
    GO:0003796    lysozyme activity    Catalysis of the hydrolysis of the beta-(1->4) linkages between N-acetylmuramic acid and N-acetyl-D-glucosamine residues in a peptidoglycan.
biological process
    GO:0016998    cell wall macromolecule catabolic process    The chemical reactions and pathways resulting in the breakdown of macromolecules that form part of a cell wall.
    GO:0019835    cytolysis    The rupture of cell membranes and the loss of cytoplasm.
    GO:0042742    defense response to bacterium    Reactions triggered in response to the presence of a bacterium that act to protect the cell or organism.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    GO:0009253    peptidoglycan catabolic process    The chemical reactions and pathways resulting in the breakdown of peptidoglycans, any of a class of glycoconjugates found in bacterial cell walls.
    GO:0019076    viral release from host cell    The dissemination of mature viral particles from the host cell, e.g. by cell lysis or the budding of virus particles from the cell membrane.
cellular component
    GO:0030430    host cell cytoplasm    The cytoplasm of a host cell.

 Visualization

(-) Interactive Views

Asymmetric/Biological 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
    HED  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    IBF  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PO4  [ 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 ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3dn3)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites 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
  3dn3
    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
  ENLYS_BPT4 | P00720
    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)
  3.2.1.17
    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
  ENLYS_BPT4 | P00720
    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
        ENLYS_BPT4 | P00720: 102l 103l 104l 107l 108l 109l 110l 111l 112l 113l 114l 115l 118l 119l 120l 122l 123l 125l 126l 127l 128l 129l 130l 131l 137l 138l 139l 140l 141l 142l 143l 144l 145l 146l 147l 148l 149l 150l 151l 152l 155l 156l 157l 158l 159l 160l 161l 162l 163l 164l 165l 166l 167l 168l 169l 170l 171l 172l 173l 174l 175l 176l 177l 178l 180l 181l 182l 183l 184l 185l 186l 187l 188l 189l 190l 191l 192l 195l 196l 197l 198l 199l 1b6i 1c60 1c61 1c62 1c63 1c64 1c65 1c66 1c67 1c68 1c69 1c6a 1c6b 1c6c 1c6d 1c6e 1c6f 1c6g 1c6h 1c6i 1c6j 1c6k 1c6l 1c6m 1c6n 1c6p 1c6q 1c6t 1ctw 1cu0 1cu2 1cu3 1cu5 1cu6 1cup 1cuq 1cv0 1cv1 1cv3 1cv4 1cv5 1cv6 1cvk 1cx6 1cx7 1d2w 1d2y 1d3f 1d3j 1d3m 1d3n 1d9w 1dya 1dyb 1dyc 1dyd 1dye 1dyf 1dyg 1epy 1g06 1g07 1g0g 1g0j 1g0k 1g0l 1g0m 1g0p 1g0q 1g1v 1g1w 1i6s 1jqu 1jtm 1jtn 1kni 1ks3 1kw5 1kw7 1ky0 1ky1 1l00 1l01 1l02 1l03 1l04 1l05 1l06 1l07 1l08 1l09 1l0j 1l0k 1l10 1l11 1l12 1l13 1l14 1l15 1l16 1l17 1l18 1l19 1l20 1l21 1l22 1l23 1l24 1l25 1l26 1l27 1l28 1l29 1l30 1l31 1l32 1l33 1l34 1l35 1l36 1l37 1l38 1l39 1l40 1l41 1l42 1l43 1l44 1l45 1l46 1l47 1l48 1l49 1l50 1l51 1l52 1l53 1l54 1l55 1l56 1l57 1l58 1l59 1l60 1l61 1l62 1l63 1l64 1l65 1l66 1l67 1l68 1l69 1l70 1l71 1l72 1l73 1l74 1l75 1l76 1l77 1l79 1l80 1l81 1l82 1l83 1l84 1l85 1l86 1l87 1l88 1l89 1l90 1l91 1l92 1l93 1l94 1l95 1l96 1l97 1l98 1l99 1lgu 1lgw 1lgx 1li2 1li3 1li6 1llh 1lpy 1lw9 1lwg 1lwk 1lyd 1lye 1lyf 1lyg 1lyh 1lyi 1lyj 1nhb 1ov5 1ov7 1ovh 1ovj 1ovk 1owy 1owz 1oyu 1p2l 1p2r 1p36 1p37 1p3n 1p46 1p56 1p5c 1p64 1p6y 1p7s 1pqd 1pqi 1pqj 1pqk 1pqm 1pqo 1qs5 1qs9 1qsb 1qsq 1qt3 1qt4 1qt5 1qt6 1qt7 1qt8 1qtb 1qtc 1qtd 1qth 1qtv 1qtz 1qud 1qug 1quh 1quo 1ssw 1ssy 1swy 1swz 1sx2 1sx7 1t6h 1t8a 1t8f 1t8g 1t97 1tla 1xep 1zur 1zwn 1zyt 200l 201l 205l 206l 209l 210l 211l 212l 213l 214l 215l 216l 217l 218l 219l 220l 221l 222l 223l 224l 225l 226l 227l 228l 229l 230l 231l 232l 233l 234l 235l 236l 237l 238l 239l 240l 241l 242l 243l 244l 245l 246l 247l 248l 249l 250l 251l 252l 253l 254l 255l 256l 257l 258l 259l 260l 261l 262l 2a4t 2b6t 2b6w 2b6x 2b6y 2b6z 2b70 2b72 2b73 2b74 2b75 2b7x 2cuu 2f2q 2f32 2f47 2huk 2hul 2hum 2igc 2l78 2lc9 2lcb 2lzm 2ntg 2nth 2o4w 2o79 2o7a 2oe4 2oe7 2oe9 2oea 2oty 2otz 2ou0 2ou8 2ou9 2q9d 2q9e 2qar 2qb0 2ray 2raz 2rb0 2rb1 2rb2 2rbn 2rbo 2rbp 2rbq 2rbr 2rbs 2rh1 3c7w 3c7y 3c7z 3c80 3c81 3c82 3c83 3c8q 3c8r 3c8s 3cdo 3cdq 3cdr 3cdt 3cdv 3d4s 3dke 3dmv 3dmx 3dmz 3dn0 3dn1 3dn2 3dn4 3dn6 3dn8 3dna 3eml 3f8v 3f9l 3fa0 3fad 3fi5 3g3v 3g3w 3g3x 3gui 3guj 3guk 3gul 3gum 3gun 3guo 3gup 3hh3 3hh4 3hh5 3hh6 3ht6 3ht7 3ht8 3ht9 3htb 3htd 3htf 3htg 3hu8 3hu9 3hua 3huk 3huq 3hwl 3jr6 3k2r 3l2x 3l64 3lzm 3ny8 3ny9 3nya 3odu 3oe0 3oe6 3oe8 3oe9 3p0g 3pbl 3pds 3qak 3run 3rze 3sb5 3sb6 3sb7 3sb8 3sb9 3sba 3sbb 3sn6 3uon 3v2w 3v2y 3vw7 4arj 4daj 4djh 4dkl 4e97 4ej4 4ekp 4ekq 4ekr 4eks 4epi 4exm 4gbr 4grv 4htt 4i7j 4i7k 4i7l 4i7m 4i7n 4i7o 4i7p 4i7q 4i7r 4i7s 4i7t 4iap 4k5y 4lde 4ldl 4ldo 4lzm 4n9n 4oo9 4phu 4rws 4s0w 4tn3 4u14 4w51 4w52 4w53 4w54 4w55 4w56 4w57 4w58 4w59 4w8f 4wtv 4xee 4xes 4yx7 4yxa 4yxc 4zwj 5b2g 5cgc 5cgd 5cxv 5d5a 5d5b 5d6l 5dgy 5dsg 5ee7 5eut 5ewx 5g27 5glh 5gli 5i14 5jdt 5jea 5jgn 5jgr 5jgu 5jgv 5jgx 5jgz 5jqh 5jws 5jwt 5jwu 5jwv 5jww 5kgr 5khz 5ki1 5ki2 5ki3 5ki8 5kig 5kii 5kim 5kio 5lwo 5lzm 5t04 5t1a 5tzr 5tzy 5vew 5vex 6lzm 7lzm

(-) Related Entries Specified in the PDB File

181l T4 LYSOZYME L99A BOUND WITH BENZENE AT ROOM TEMPERATURE
3dke
3dmv
3dmx
3dmz
3dn0
3dn1
3dn2
3dn4
3dn6
3dn8
3dna