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 PROTEIN FROM NEISSERIA MENINGITIDIS MC58
 
Authors :  R. Zhang, K. Tan, L. Volkart, M. Bargassa, A. Joachimiak, Midwest Cent Structural Genomics (Mcsg)
Date :  15 Jul 10  (Deposition) - 22 Sep 10  (Release) - 22 Sep 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
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, L. Volkart, M. Bargassa, A. Joachimiak
The Crystal Structure Of Functionally Unknown Protein 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: PMCSG7
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Gene: NMB0500, NMB1774
    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  (5, 27)

Asymmetric/Biological Unit (5, 27)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2MLY12Mod. Amino AcidN-DIMETHYL-LYSINE
3MSE9Mod. Amino AcidSELENOMETHIONINE
4PEG3Ligand/IonDI(HYDROXYETHYL)ETHER
5SO42Ligand/IonSULFATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:16BINDING SITE FOR RESIDUE PEG A 126
2AC2SOFTWAREASP A:74 , ASN A:76 , GLU B:56 , ASN B:60 , HOH B:219BINDING SITE FOR RESIDUE PEG A 127
3AC3SOFTWAREMLY A:75 , ASN A:76 , PHE A:77 , MLY A:78BINDING SITE FOR RESIDUE SO4 A 128
4AC4SOFTWAREPHE A:118 , SER A:119 , PRO A:121 , HOH A:178 , PHE B:77 , HOH B:208BINDING SITE FOR RESIDUE PEG B 126
5AC5SOFTWAREMLY B:75 , ASN B:76 , PHE B:77 , MLY B:78BINDING SITE FOR RESIDUE SO4 B 127
6AC6SOFTWAREASP B:51 , PHE B:54 , LYS B:55BINDING SITE FOR RESIDUE ACT B 128

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3NYM)

(-) 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:124
 aligned with Q9JS17_NEIMB | Q9JS17 from UniProtKB/TrEMBL  Length:125

    Alignment length:124
                             1                                                                                                                          
                             |       9        19        29        39        49        59        69        79        89        99       109       119    
         Q9JS17_NEIMB     - -METLNDIKKILINVGLYQGFDLTDPKVSEEVNHETANMKWIKDYTSDGNWDNEFKEDLKNFLDYMEVCQLALNDKNFKIASNSLFMAMIYAGNLSLIFDSIKTDISTLLSAEYKKNSFSWPSL 123
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhh.....hhhhhh.ee....ee..........hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nym A   0 AmETLNDIkKILINVGLYQGFDLTDPKVSEEVNHETANmkWIkDYTSDGNWDNEFKEDLkNFLDYmEVCQLALNDkNFkIASNSLFmAmIYAGNLSLIFDSIKTDISTLLSAEYKKNSFSWPSL 123
                             |      |9        19        29        39  |     49        59     |  69     |  79      | 89        99       109       119    
                             |      8-MLY                        38-MSE               59-MLY |        75-MLY     86-MSE                                 
                             1-MSE                                39-MLY                    65-MSE       78-MLY    88-MSE                               
                                                                     42-MLY                                                                             


Chain B from PDB  Type:PROTEIN  Length:123
 aligned with Q9JS17_NEIMB | Q9JS17 from UniProtKB/TrEMBL  Length:125

    Alignment length:123
                                    11        21        31        41        51        61        71        81        91       101       111       121   
         Q9JS17_NEIMB     2 ETLNDIKKILINVGLYQGFDLTDPKVSEEVNHETANMKWIKDYTSDGNWDNEFKEDLKNFLDYMEVCQLALNDKNFKIASNSLFMAMIYAGNLSLIFDSIKTDISTLLSAEYKKNSFSWPSLD 124
               SCOP domains --------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhh.....hhhhhh.ee....ee..........hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nym B   2 ETLNDIkKILINVGLYQGFDLTDPKVSEEVNHETANmkWIkDYTSDGNWDNEFKEDLkNFLDYmEVCQLALNDkNFkIASNSLFmAmIYAGNLSLIFDSIKTDISTLLSAEYKKNSFSWPSLD 124
                                  | 11        21        31      ||41|       51       |61   |    71   |  | 81    | | 91       101       111       121   
                                  8-MLY                        38-MSE               59-MLY |        75-MLY     86-MSE                                  
                                                                39-MLY                    65-MSE       78-MLY    88-MSE                                
                                                                   42-MLY
   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 3NYM)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3NYM)

 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
    ACT  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MLY  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PEG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ 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 3nym)
 

(-) 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
  3nym
    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
  Q9JS17_NEIMB | Q9JS17
    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
  Q9JS17_NEIMB | Q9JS17
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 3NYM)

(-) Related Entries Specified in the PDB File

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