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
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)

(-) Description

Title :  TAILSPIKE PROTEIN DOUBLE MUTANT D339N/E372Q OF E. COLI BACTERIOPHAGE HK620 IN COMPLEX WITH HEXASACCHARIDE
 
Authors :  U. Gohlke, N. K. Broeker, U. Heinemann, R. Seckler, S. Barbirz
Date :  16 Jan 15  (Deposition) - 27 Jan 16  (Release) - 27 Jan 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.59
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (3x)
Keywords :  Beta Helix, Protein-Carbohydrate Complex, Pectin Lyase Fold, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  U. Gohlke, N. K. Broeker, S. Kunstmann, M. Santer, U. Heinemann, R. Lipowski, R. Seckler, S. Barbirz
Enthalpic Cost Of Water Removal From A Hydrophobic Glucose Binding Cavity On Hk620 Tailspike Protein.
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TAIL SPIKE PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: PET11D
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Fragment: HEAD BINDING, UNP RESIDUES 115-710
    Mutation: YES
    Organism Scientific: ENTEROBACTERIA PHAGE HK620
    Organism Taxid: 155148

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (3x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (8, 16)

Asymmetric Unit (8, 16)
No.NameCountTypeFull Name
1FMT5Ligand/IonFORMIC ACID
2GLA1Ligand/IonALPHA D-GALACTOSE
3GLC2Ligand/IonALPHA-D-GLUCOSE
4NA3Ligand/IonSODIUM ION
5NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
6NDG1Ligand/Ion2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
7RAM1Ligand/IonALPHA-L-RHAMNOSE
8TRS1Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Biological Unit 1 (7, 39)
No.NameCountTypeFull Name
1FMT15Ligand/IonFORMIC ACID
2GLA3Ligand/IonALPHA D-GALACTOSE
3GLC6Ligand/IonALPHA-D-GLUCOSE
4NA-1Ligand/IonSODIUM ION
5NAG6Ligand/IonN-ACETYL-D-GLUCOSAMINE
6NDG3Ligand/Ion2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
7RAM3Ligand/IonALPHA-L-RHAMNOSE
8TRS3Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREVAL A:568 , ASN A:569 , TYR A:597 , ASP A:670 , ILE A:693 , ARG A:697 , HOH A:1141 , HOH A:1167 , HOH A:1197 , HOH A:1337binding site for residue TRS A 1008
02AC2SOFTWAREARG A:140 , ASP A:144 , HOH A:1109 , HOH A:1362binding site for residue FMT A 1009
03AC3SOFTWARETYR A:597 , ASN A:625 , LEU A:669 , ASP A:670 , HOH A:1114 , HOH A:1304binding site for residue FMT A 1010
04AC4SOFTWAREASP A:541 , LYS A:542 , ASN A:544 , GLN A:575 , HOH A:1105 , HOH A:1133 , HOH A:1370binding site for residue FMT A 1011
05AC5SOFTWAREGLY A:167 , TYR A:197 , THR A:198 , TYR A:200 , HOH A:1159 , HOH A:1203 , HOH A:1465binding site for residue FMT A 1012
06AC6SOFTWAREARG A:505 , HOH A:1274 , HOH A:1417binding site for residue FMT A 1013
07AC7SOFTWAREALA A:565 , SER A:592 , GLN A:594 , HOH A:1611 , HOH A:1637 , HOH A:1650binding site for residue NA A 1014
08AC8SOFTWAREVAL A:483 , THR A:512 , ASN A:517 , HOH A:1297 , HOH A:1594 , HOH A:1716binding site for residue NA A 1015
09AC9SOFTWAREGLY A:211 , RAM A:1001 , HOH A:1528 , HOH A:1579 , HOH A:1654binding site for residue NA A 1016
10AD1SOFTWAREGLY A:211 , HIS A:212 , GLN A:242 , LEU A:282 , THR A:307 , TRP A:308 , THR A:311 , TRP A:314 , ASN A:315 , ASN A:339 , HIS A:340 , SER A:341 , TYR A:344 , ASN A:346 , GLN A:372 , TYR A:393 , VAL A:395 , HIS A:397 , GLU A:400 , LEU A:427 , GLY A:428 , ASP A:430 , GLY A:468 , PRO A:469 , ASP A:470 , ASN A:471 , NA A:1016 , HOH A:1104 , HOH A:1115 , HOH A:1127 , HOH A:1209 , HOH A:1217 , HOH A:1221 , HOH A:1251 , HOH A:1282 , HOH A:1292 , HOH A:1353 , HOH A:1366 , HOH A:1398 , HOH A:1411 , HOH A:1437 , HOH A:1440 , HOH A:1479 , HOH A:1487 , HOH A:1510 , HOH A:1528 , HOH A:1547 , HOH A:1573 , HOH A:1579binding site for Poly-Saccharide residues RAM A 1001 through NAG A 1007

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4XOP)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4XOP)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4XOP)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4XOP)

(-) Exons   (0, 0)

(no "Exon" information available for 4XOP)

(-) 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:596
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhh.hhhhh...hhhhh.......hhhhhh.....hhh................hhhhhhhhhhhhhhh...................hhhhhhh.....................hhhh.............hhhhh...........................................................................................................hhhhh.............................hhhhh.........................................................................................................................................................................................................................hhhhh...................................................................................... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4xop A 114 FRAIIESPEGAGHVGYQYRRNTGSTMRMVSDVLDERVSLWDFHCDPSGNVIQPGPNVDSRQYLQAAIDYVSSNGGGTITIPAGYTWYLGSYGVGGIAGHSGIIQLRSNVNLNIEGRIHLSPFFDLKPFQVFVGFDNGDPASSGNLENCHIYGHGVVDFGGYEFGASSQLRNGVAFGRSYNCSVTGITFQNGDVTWAITLGWNGYGSNCYVRKCRFINLVNSSVNANHSTVYVNCPYSGVESCYFSMSSSFARNIACSVQLHQHDTFYRGSTVNGYCRGAYVVMHAAEAAGAGSYAYNMQVENNIAVIYGQFVILGSDVTATVSGHLNDVIVSGNIVSIGERAAFSAPFGAFIDIGPDNSGASNVQDIQRVLVTGNSFYAPANITDSAAITLRANLNGCTFIANNFDCRYMVYNAPGTTSPVVQNLVWDKSNVIGGTHANQRAGQNLFDMQFASVVNSTIEVQLSCEDLSMFSCILFPASCQLSYSKITVDSAWTKSMSNTAVFEGNQQAGANVYVSYPATVNLTSYNTQGAVPFFSTDTNYAWVTSAYSLSINENLDFSPPATYTNKANGQLVGVGYNEIGGVRSVSVRLMLQRQV 709
                                   123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633       643       653       663       673       683       693       703
   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  (0, 0)

(no "SCOP Domain" information available for 4XOP)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4XOP)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4XOP)

(-) Gene Ontology  (1, 1)

Asymmetric Unit(hide GO term definitions)

 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 ]
    GLA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GLC  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NAG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NDG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    RAM  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    TRS  [ 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 ]
    AD1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4xop)
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ 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 ](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
  4xop
    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
  Q9AYY6_BPHK6 | Q9AYY6
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    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
  Q9AYY6_BPHK6 | Q9AYY6
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q9AYY6_BPHK6 | Q9AYY6: 2vji 2vjj 2x6w 2x6x 2x6y 2x85 4avz 4xkv 4xkw 4xl9 4xla 4xlc 4xle 4xlf 4xlh 4xm3 4xmy 4xn0 4xn3 4xnf 4xon 4xor 4xot 4xqf 4xqh 4xqi 4xr6 4yej 4yel

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4XOP)