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
(-)Biological Unit 3
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)
Image Biological Unit 3
Biological Unit 3  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF E. COLI PHOSPHATASE YRBI, WITH MG, TETRAGONAL FORM
 
Authors :  O. V. Tsodikov, T. Biswas
Date :  22 Jun 09  (Deposition) - 01 Sep 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.06
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H
Biol. Unit 1:  E,F,G,H  (1x)
Biol. Unit 2:  A,B,C,D  (1x)
Biol. Unit 3:  A,B,C,D,E,F,G,H  (1x)
Keywords :  Yrbi, Kdsc, Phosphatase, Hydrolase, Lipopolysaccharide Biosynthesis, Magnesium (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Biswas, L. Yi, P. Aggarwal, J. Wu, J. R. Rubin, J. A. Stuckey, R. W. Woodard, O. V. Tsodikov
The Tail Of Kdsc: Conformational Changes Control The Activity Of A Haloacid Dehalogenase Superfamily Phosphatase
J. Biol. Chem. V. 284 30594 2009
PubMed-ID: 19726684  |  Reference-DOI: 10.1074/JBC.M109.012278

(-) Compounds

Molecule 1 - 3-DEOXY-D-MANNO-OCTULOSONATE 8-PHOSPHATE PHOSPHATASE
    Chains: A, B, C, D, E, F, G, H
    EC Number: 3.1.3.45
    Engineered: YES
    Gene: YRBI
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 37762
    Strain: B
    Synonym: KDO 8-P PHOSPHATASE

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : ABCDEFGH
Biological Unit 1 (1x):     EFGH
Biological Unit 2 (1x): ABCD    
Biological Unit 3 (1x): ABCDEFGH

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 13)

Asymmetric Unit (2, 13)
No.NameCountTypeFull Name
1CL5Ligand/IonCHLORIDE ION
2MG8Ligand/IonMAGNESIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2MG-1Ligand/IonMAGNESIUM ION
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:32 , ASP A:34 , ASP A:125BINDING SITE FOR RESIDUE MG A 201
02AC2SOFTWARESER A:187 , ASP B:32 , ASP B:34 , ASP B:125BINDING SITE FOR RESIDUE MG B 202
03AC3SOFTWAREASP C:32 , ASP C:34 , ASP C:125BINDING SITE FOR RESIDUE MG C 203
04AC4SOFTWARESER C:187 , ASP D:32 , ASP D:34 , ASP D:125BINDING SITE FOR RESIDUE MG D 204
05AC5SOFTWAREASP E:32 , ASP E:34 , ASP E:125BINDING SITE FOR RESIDUE MG E 205
06AC6SOFTWARESER E:187 , ASP F:32 , ASP F:34 , ASP F:125BINDING SITE FOR RESIDUE MG F 206
07AC7SOFTWAREASP G:32 , ASP G:34 , ASP G:125BINDING SITE FOR RESIDUE MG G 207
08AC8SOFTWARESER G:187 , ASP H:32 , ASP H:34 , ASP H:125BINDING SITE FOR RESIDUE MG H 208
09AC9SOFTWARESER A:187 , ASP B:32 , GLY B:77 , LYS B:102BINDING SITE FOR RESIDUE CL B 204
10BC1SOFTWAREASP D:32 , GLY D:77 , LYS D:102BINDING SITE FOR RESIDUE CL D 205
11BC2SOFTWARESER E:187 , ASP F:32 , GLY F:77 , LYS F:102 , ILE F:128BINDING SITE FOR RESIDUE CL F 189
12BC3SOFTWAREASP G:32 , LYS G:102 , ILE G:128BINDING SITE FOR RESIDUE CL G 189
13BC4SOFTWAREGLY H:77 , LYS H:102BINDING SITE FOR RESIDUE CL H 189

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3HYC)

(-) 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:181
 aligned with KDSC_ECOL6 | P67653 from UniProtKB/Swiss-Prot  Length:188

    Alignment length:181
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187 
           KDSC_ECOL6     8 LATCYGPVSADVMAKAENIRLLILDVDGVLSDGLIYMGNNGEELKAFNVRDGYGIRCALTSDIEVAIITGRKAKLVEDRCATLGITHLYQGQSNKLIAFSDLLEKLAIAPENVAYVGDDLIDWPVMEKVGLSVAVADAHPLLIPRADYVTRIAGGRGAVREVCDLLLLAQGKLDEAKGQSI 188
               SCOP domains d3hyca_ A: automated matches                                                                                                                                                          SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee..ee.hhhhhhhhhh..eeee.........eeeee....eeeeeehhhhhhhhhhhhh..eeeeee...hhhhhhhhhhhh..eeee....hhhhhhhhhhh...hhh.eeeee.hhhhhhhhh...eeee.......hhhhh.ee.......hhhhhhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3hyc A   8 LATCYGPVSADVMAKAENIRLLILDVDGVLSDGLIYMGNNGEELKAFNVRDGYGIRCALTSDIEVAIITGRKAKLVEDRCATLGITHLYQGQSNKLIAFSDLLEKLAIAPENVAYVGDDLIDWPVMEKVGLSVAVADAHPLLIPRADYVTRIAGGRGAVREVCDLLLLAQGKLDEAKGQSI 188
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187 


Chain B from PDB  Type:PROTEIN  Length:174
 aligned with KDSC_ECOL6 | P67653 from UniProtKB/Swiss-Prot  Length:188

    Alignment length:174
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177    
           KDSC_ECOL6     8 LATCYGPVSADVMAKAENIRLLILDVDGVLSDGLIYMGNNGEELKAFNVRDGYGIRCALTSDIEVAIITGRKAKLVEDRCATLGITHLYQGQSNKLIAFSDLLEKLAIAPENVAYVGDDLIDWPVMEKVGLSVAVADAHPLLIPRADYVTRIAGGRGAVREVCDLLLLAQGKLD 181
               SCOP domains d3hycb_ B: automated matches                                                                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........hhhhhhhhhh..eeee.........eeeee....eeeeeehhhhhhhhhhhh...eeeee....hhhhhhhhhhhh..eee....hhhhhhhhhhhhh..hhh.eeeee.hhhhhhhhhhh.eeee.......hhhhh.ee.......hhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3hyc B   8 LATCYGPVSADVMAKAENIRLLILDVDGVLSDGLIYMGNNGEELKAFNVRDGYGIRCALTSDIEVAIITGRKAKLVEDRCATLGITHLYQGQSNKLIAFSDLLEKLAIAPENVAYVGDDLIDWPVMEKVGLSVAVADAHPLLIPRADYVTRIAGGRGAVREVCDLLLLAQGKLD 181
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177    


Chain C from PDB  Type:PROTEIN  Length:181
 aligned with KDSC_ECOL6 | P67653 from UniProtKB/Swiss-Prot  Length:188

    Alignment length:181
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187 
           KDSC_ECOL6     8 LATCYGPVSADVMAKAENIRLLILDVDGVLSDGLIYMGNNGEELKAFNVRDGYGIRCALTSDIEVAIITGRKAKLVEDRCATLGITHLYQGQSNKLIAFSDLLEKLAIAPENVAYVGDDLIDWPVMEKVGLSVAVADAHPLLIPRADYVTRIAGGRGAVREVCDLLLLAQGKLDEAKGQSI 188
               SCOP domains d3hycc_ C: automated matches                                                                                                                                                          SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhh..eeee.........eeeee....eeeeeehhhhhhhhhhhh...eeeee....hhhhhhhhhhhh..eee.....hhhhhhhhhhhhh.hhh.eeeee.hhhhhhhhh...eeee.......hhhhh.ee.......hhhhhhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3hyc C   8 LATCYGPVSADVMAKAENIRLLILDVDGVLSDGLIYMGNNGEELKAFNVRDGYGIRCALTSDIEVAIITGRKAKLVEDRCATLGITHLYQGQSNKLIAFSDLLEKLAIAPENVAYVGDDLIDWPVMEKVGLSVAVADAHPLLIPRADYVTRIAGGRGAVREVCDLLLLAQGKLDEAKGQSI 188
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187 


Chain D from PDB  Type:PROTEIN  Length:176
 aligned with KDSC_ECOL6 | P67653 from UniProtKB/Swiss-Prot  Length:188

    Alignment length:176
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177      
           KDSC_ECOL6     8 LATCYGPVSADVMAKAENIRLLILDVDGVLSDGLIYMGNNGEELKAFNVRDGYGIRCALTSDIEVAIITGRKAKLVEDRCATLGITHLYQGQSNKLIAFSDLLEKLAIAPENVAYVGDDLIDWPVMEKVGLSVAVADAHPLLIPRADYVTRIAGGRGAVREVCDLLLLAQGKLDEA 183
               SCOP domains d3hycd_ D: automated matches                                                                                                                                                     SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhh..eeee.........eeeee....eeeeeehhhhhhhhhhhhh..eeeee....hhhhhhhhhhhh..eee....hhhhhhhhhhhhhh.hhh.eeeee.hhhhhhhhh...eeee.......hhhhh.ee.......hhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3hyc D   8 LATCYGPVSADVMAKAENIRLLILDVDGVLSDGLIYMGNNGEELKAFNVRDGYGIRCALTSDIEVAIITGRKAKLVEDRCATLGITHLYQGQSNKLIAFSDLLEKLAIAPENVAYVGDDLIDWPVMEKVGLSVAVADAHPLLIPRADYVTRIAGGRGAVREVCDLLLLAQGKLDEA 183
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177      


Chain E from PDB  Type:PROTEIN  Length:181
 aligned with KDSC_ECOL6 | P67653 from UniProtKB/Swiss-Prot  Length:188

    Alignment length:181
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187 
           KDSC_ECOL6     8 LATCYGPVSADVMAKAENIRLLILDVDGVLSDGLIYMGNNGEELKAFNVRDGYGIRCALTSDIEVAIITGRKAKLVEDRCATLGITHLYQGQSNKLIAFSDLLEKLAIAPENVAYVGDDLIDWPVMEKVGLSVAVADAHPLLIPRADYVTRIAGGRGAVREVCDLLLLAQGKLDEAKGQSI 188
               SCOP domains d3hyce_ E: automated matches                                                                                                                                                          SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhh...eeee.........eeeee....eeeeeehhhhhhhhhhhhh..eeeeee...hhhhhhhhhhhh..eeee....hhhhhhhhhhhhh.hhh.eeeee.hhhhhhhhhhh.eeee.......hhhhh.ee.......hhhhhhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3hyc E   8 LATCYGPVSADVMAKAENIRLLILDVDGVLSDGLIYMGNNGEELKAFNVRDGYGIRCALTSDIEVAIITGRKAKLVEDRCATLGITHLYQGQSNKLIAFSDLLEKLAIAPENVAYVGDDLIDWPVMEKVGLSVAVADAHPLLIPRADYVTRIAGGRGAVREVCDLLLLAQGKLDEAKGQSI 188
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187 


Chain F from PDB  Type:PROTEIN  Length:181
 aligned with KDSC_ECOL6 | P67653 from UniProtKB/Swiss-Prot  Length:188

    Alignment length:181
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187 
           KDSC_ECOL6     8 LATCYGPVSADVMAKAENIRLLILDVDGVLSDGLIYMGNNGEELKAFNVRDGYGIRCALTSDIEVAIITGRKAKLVEDRCATLGITHLYQGQSNKLIAFSDLLEKLAIAPENVAYVGDDLIDWPVMEKVGLSVAVADAHPLLIPRADYVTRIAGGRGAVREVCDLLLLAQGKLDEAKGQSI 188
               SCOP domains d3hycf_ F: automated matches                                                                                                                                                          SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhh...eeee.........eeee.....eeeeeehhhhhhhhhhhhh..eeeee....hhhhhhhhhhhh..eee.....hhhhhhhhhhhh..hhh.eeeee....hhhhhh...eeee.......hhhhh.ee.......hhhhhhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3hyc F   8 LATCYGPVSADVMAKAENIRLLILDVDGVLSDGLIYMGNNGEELKAFNVRDGYGIRCALTSDIEVAIITGRKAKLVEDRCATLGITHLYQGQSNKLIAFSDLLEKLAIAPENVAYVGDDLIDWPVMEKVGLSVAVADAHPLLIPRADYVTRIAGGRGAVREVCDLLLLAQGKLDEAKGQSI 188
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187 


Chain G from PDB  Type:PROTEIN  Length:181
 aligned with KDSC_ECOL6 | P67653 from UniProtKB/Swiss-Prot  Length:188

    Alignment length:181
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187 
           KDSC_ECOL6     8 LATCYGPVSADVMAKAENIRLLILDVDGVLSDGLIYMGNNGEELKAFNVRDGYGIRCALTSDIEVAIITGRKAKLVEDRCATLGITHLYQGQSNKLIAFSDLLEKLAIAPENVAYVGDDLIDWPVMEKVGLSVAVADAHPLLIPRADYVTRIAGGRGAVREVCDLLLLAQGKLDEAKGQSI 188
               SCOP domains d3hycg_ G: automated matches                                                                                                                                                          SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhh..eeee.........eeeee....eeeeeehhhhhhhhhhhhh..eeeeee...hhhhhhhhhhhh..eeee....hhhhhhhhhhhhh.hhh.eeeee.hhhhhhhhh...eeee.......hhhhh.ee.......hhhhhhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3hyc G   8 LATCYGPVSADVMAKAENIRLLILDVDGVLSDGLIYMGNNGEELKAFNVRDGYGIRCALTSDIEVAIITGRKAKLVEDRCATLGITHLYQGQSNKLIAFSDLLEKLAIAPENVAYVGDDLIDWPVMEKVGLSVAVADAHPLLIPRADYVTRIAGGRGAVREVCDLLLLAQGKLDEAKGQSI 188
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187 


Chain H from PDB  Type:PROTEIN  Length:181
 aligned with KDSC_ECOL6 | P67653 from UniProtKB/Swiss-Prot  Length:188

    Alignment length:181
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187 
           KDSC_ECOL6     8 LATCYGPVSADVMAKAENIRLLILDVDGVLSDGLIYMGNNGEELKAFNVRDGYGIRCALTSDIEVAIITGRKAKLVEDRCATLGITHLYQGQSNKLIAFSDLLEKLAIAPENVAYVGDDLIDWPVMEKVGLSVAVADAHPLLIPRADYVTRIAGGRGAVREVCDLLLLAQGKLDEAKGQSI 188
               SCOP domains d3hych_ H: automated matches                                                                                                                                                          SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhh..eeee.........eeeee....eeeeeehhhhhhhhhhhhh..eeeee....hhhhhhhhhhhh..eee....hhhhhhhhhhhhhh.hhh.eeeee.hhhhhhhhh...eeee.......hhhhh.ee.......hhhhhhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3hyc H   8 LATCYGPVSADVMAKAENIRLLILDVDGVLSDGLIYMGNNGEELKAFNVRDGYGIRCALTSDIEVAIITGRKAKLVEDRCATLGITHLYQGQSNKLIAFSDLLEKLAIAPENVAYVGDDLIDWPVMEKVGLSVAVADAHPLLIPRADYVTRIAGGRGAVREVCDLLLLAQGKLDEAKGQSI 188
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187
   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, 8)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3HYC)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D,E,F,G,H   (KDSC_ECOL6 | P67653)
molecular function
    GO:0019143    3-deoxy-manno-octulosonate-8-phosphatase activity    Catalysis of the reaction: 8-phospho-3-deoxy-D-manno-oct-2-ulosonate + H(2)O = 3-deoxy-D-manno-octulosonate + phosphate.
    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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0016311    dephosphorylation    The process of removing one or more phosphoric (ester or anhydride) residues from a molecule.
    GO:0009103    lipopolysaccharide biosynthetic process    The chemical reactions and pathways resulting in the formation of lipopolysaccharides, any of a group of related, structurally complex components of the outer membrane of Gram-negative bacteria.

 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
    CL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MG  [ 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 ]
    BC3  [ RasMol ]  +environment [ RasMol ]
    BC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3hyc)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]
    Biological Unit 3  [ 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 | Biol. Unit 3 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
  3hyc
    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
  KDSC_ECOL6 | P67653
    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)
  3.1.3.45
    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
  KDSC_ECOL6 | P67653
    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
        KDSC_ECOL6 | P67653: 2r8e 2r8x 2r8y 2r8z 3i6b

(-) Related Entries Specified in the PDB File

2r8x CRYSTAL STRUCTURE OF YRBI PHOSPHATASE FROM ESCHERICHIA COLI
2r8y CRYSTAL STRUCTURE OF YRBI PHOSPHATASE FROM ESCHERICHIA COLI IN A COMPLEX WITH CA
2r8z CRYSTAL STRUCTURE OF YRBI PHOSPHATASE FROM ESCHERICHIA COLI IN COMPLEX WITH A PHOSPHATE AND A CALCIUM ION