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 :  THE CRYSTAL STRUCTURE OF FUNCTIONALLY UNKNOWN CONSERVED PROTEIN DOMAIN FROM NEISSERIA MENINGITIDIS MC58
 
Authors :  R. Zhang, K. Tan, H. Li, G. Cobb, A. Joachimiak, Midwest Center For St Genomics (Mcsg)
Date :  18 Aug 10  (Deposition) - 22 Sep 10  (Release) - 22 Sep 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.99
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Structural Genomics, Psi-2, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Zhang, K. Tan, H. Li, G. Cobb, A. Joachimiak
The Crystal Structure Of Functionally Unknown Conserved Protein Domain From Neisseria Meningitidis Mc58
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - UNCHARACTERIZED PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG19
    Expression System Strain: PPK1037
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: SEQUENCE DATABASE RESIDUES 24-176
    Gene: NMB0537
    Organism Scientific: NEISSERIA MENINGITIDIS SEROGROUP B
    Organism Taxid: 491
    Strain: MC58

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 12)

Asymmetric/Biological Unit (4, 12)
No.NameCountTypeFull Name
1ADN2Ligand/IonADENOSINE
2GOL1Ligand/IonGLYCEROL
3MSE8Mod. Amino AcidSELENOMETHIONINE
4PEG1Ligand/IonDI(HYDROXYETHYL)ETHER

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:65 , MSE A:70 , ASN A:71 , HIS A:91 , ARG A:93 , PHE A:94 , PRO A:95 , ASP A:173 , HOH A:180BINDING SITE FOR RESIDUE ADN A 2
2AC2SOFTWARELEU A:73 , LYS A:74 , ASP A:77 , TYR A:85BINDING SITE FOR RESIDUE GOL A 1
3AC3SOFTWAREALA A:84 , ILE A:87 , ASP A:88BINDING SITE FOR RESIDUE PEG A 177
4AC4SOFTWAREARG A:152 , ILE B:65 , ARG B:69 , MSE B:70 , ASN B:71 , HIS B:91 , ARG B:93 , PRO B:95 , MSE B:155 , THR B:170 , GLU B:172 , ASP B:173 , HOH B:217 , HOH B:226BINDING SITE FOR RESIDUE ADN B 1

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3OI8)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3OI8)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3OI8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3OI8)

(-) Exons   (0, 0)

(no "Exon" information available for 3OI8)

(-) 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:156
 aligned with Q9K0P8_NEIMB | Q9K0P8 from UniProtKB/TrEMBL  Length:274

    Alignment length:156
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170      
         Q9K0P8_NEIMB    21 EPDSAEDVLNLLRQAHEQEVFDADTLLRLEKVLDFSDLEVRDAMITRSRMNVLKENDSIERITAYVIDTAHSRFPVIGEDKDEVLGILHAKDLLKYMFNPEQFHLKSILRPAVFVPEGKSLTALLKEFREQRNHMAIVIDEYGGTSGLVTFEDIIE 176
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh.ee.hhh..ee...hhhhhhhhhhhhh..eeeee......eeeeee.hhhhhhh.hhhhhhhhhhh....eee...hhhhhhhhhhhh...eeeee.....eeeeeehhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3oi8 A  21 SNASAEDVLNLLRQAHEQEVFDADTLLRLEKVLDFSDLEVRDAmITRSRmNVLKENDSIERITAYVIDTAHSRFPVIGEDKDEVLGILHAKDLLKYmFNPEQFHLKSILRPAVFVPEGKSLTALLKEFREQRNHmAIVIDEYGGTSGLVTFEDIIE 176
                                    30        40        50        60   |    70        80        90       100       110      |120       130       140       150    |  160       170      
                                                                      64-MSE |                                            117-MSE                               155-MSE                 
                                                                            70-MSE                                                                                                      


Chain B from PDB  Type:PROTEIN  Length:154
 aligned with Q9K0P8_NEIMB | Q9K0P8 from UniProtKB/TrEMBL  Length:274

    Alignment length:154
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171    
         Q9K0P8_NEIMB    22 PDSAEDVLNLLRQAHEQEVFDADTLLRLEKVLDFSDLEVRDAMITRSRMNVLKENDSIERITAYVIDTAHSRFPVIGEDKDEVLGILHAKDLLKYMFNPEQFHLKSILRPAVFVPEGKSLTALLKEFREQRNHMAIVIDEYGGTSGLVTFEDII 175
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -------------------------------------------------------------------------------------------------------CBS-3oi8B01 B:125-175                               Pfam domains (1)
           Pfam domains (2) -------------------------------------------------------------------------------------------------------CBS-3oi8B02 B:125-175                               Pfam domains (2)
           Pfam domains (3) -------------------------------------------------------------------------------------------------------CBS-3oi8B03 B:125-175                               Pfam domains (3)
           Pfam domains (4) -------------------------------------------------------------------------------------------------------CBS-3oi8B04 B:125-175                               Pfam domains (4)
         Sec.struct. author hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh...hhhhhhee.hhh..ee...hhhhhhhhhhhhh..eeeee......eeeeee.hhhhhhh.hhhhhhhhhh.....eee...hhhhhhhhhhhhh..eeeee.....eeeeeehhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3oi8 B  22 NASAEDVLNLLRQAHEQEVFDADTLLRLEKVLDFSDLEVRDAmITRSRmNVLKENDSIERITAYVIDTAHSRFPVIGEDKDEVLGILHAKDLLKYmFNPEQFHLKSILRPAVFVPEGKSLTALLKEFREQRNHmAIVIDEYGGTSGLVTFEDII 175
                                    31        41        51        61  |     71        81        91       101       111     | 121       131       141       151   |   161       171    
                                                                     64-MSE |                                            117-MSE                               155-MSE                
                                                                           70-MSE
   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 3OI8)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3OI8)

(-) Pfam Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: CBS] (51)
(-)
Family: CBS (51)
(-)
Neisseria meningitidis serogroup B (1)
1aCBS-3oi8B01B:125-175
1bCBS-3oi8B02B:125-175
1cCBS-3oi8B03B:125-175
1dCBS-3oi8B04B:125-175

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q9K0P8_NEIMB | Q9K0P8)
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:0050660    flavin adenine dinucleotide binding    Interacting selectively and non-covalently with FAD, flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes, in either the oxidized form, FAD, or the reduced form, FADH2.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0016614    oxidoreductase activity, acting on CH-OH group of donors    Catalysis of an oxidation-reduction (redox) reaction in which a CH-OH group act as a hydrogen or electron donor and reduces a hydrogen or electron acceptor.
biological process
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.

 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
    ADN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PEG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3oi8)
 

(-) 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
  3oi8
    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
  Q9K0P8_NEIMB | Q9K0P8
    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
  Q9K0P8_NEIMB | Q9K0P8
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q9K0P8_NEIMB | Q9K0P8: 2pli

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3OI8)