Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Biological Unit 1
(-)Biological Unit 2
(-)Biological Unit 3
(-)Biological Unit 4
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)
Image Biological Unit 3
Biological Unit 3  (Jmol Viewer)
Image Biological Unit 4
Biological Unit 4  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF THE NMB1088 PROTEIN FROM NEISSERIA MENINGITIDIS. NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET MR91
 
Authors :  F. Forouhar, H. Neely, J. Seetharaman, L. Mao, Y. Fang, R. Xiao, L. A. Owen, M. Maglaqui, K. Cunningham, M. C. Baran, T. B. Acton, G. T. Montelione, L. Tong, J. F. Hunt, Northeast Structural Genomics Consortium (Nesg)
Date :  30 Nov 07  (Deposition) - 18 Dec 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Biol. Unit 3:  D,E,F  (1x)
Biol. Unit 4:  F,G,H  (1x)
Keywords :  Alpha-Beta Protein, Structural Genomics, Psi-2, Protein Structure Initiative, Northeast Structural Genomics Consortium, Nesg, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. Forouhar, H. Neely, J. Seetharaman, L. Mao, Y. Fang, R. Xiao, L. A. Owen, M. Maglaqui, K. Cunningham, M. C. Baran, T. B. Acton, G. T. Montelione, L. Tong, J. F. Hunt
Crystal Structure Of The Nmb1088 Protein From Neisseria Meningitidis.
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - UPF0339 PROTEIN NMB1088
    Chains: A, B, C, D, E, F, G, H
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21
    Expression System Strain: BL21(DE3)+MAGIC
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: NMB1088, 903505
    Organism Scientific: NEISSERIA MENINGITIDIS MC58
    Organism Taxid: 122586
    Strain: MC58 / SEROGROUP B

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : ABCDEFGH
Biological Unit 1 (1x): AB      
Biological Unit 2 (1x):   CD    
Biological Unit 3 (1x):    DEF  
Biological Unit 4 (1x):      FGH

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 8)

Asymmetric Unit (1, 8)
No.NameCountTypeFull Name
1MSE8Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1MSE2Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1MSE2Mod. Amino AcidSELENOMETHIONINE
Biological Unit 3 (1, 3)
No.NameCountTypeFull Name
1MSE3Mod. Amino AcidSELENOMETHIONINE
Biological Unit 4 (1, 3)
No.NameCountTypeFull Name
1MSE3Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 3BID)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3BID)

(-) 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:58
 aligned with Y1088_NEIMB | Q7DDI1 from UniProtKB/Swiss-Prot  Length:56

    Alignment length:58
                                                                                  56  
                                    10        20        30        40        50     |  
           Y1088_NEIMB    1 MYFEIYKDAKGEYRWRLKAANHEIIAQGEGYTSKQNCQHAVDLLKSTTAATPVKEV--  -
               SCOP domains d3bida1 A:1-56 Uncharacterized protein NMB1088          -- SCOP domains
               CATH domains -3bidA01 A:2-47 YegP-like domains              ----------- CATH domains
               Pfam domains ---------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.....eeeeee.....eeee.....hhhhhhhhhhhhhh......eee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------- Transcript
                  3bid A  1 mYFEIYKDAKGEYRWRLKAANHEIIAQGEGYTSKQNCQHAVDLLKSTTAATPVKEVLE 58
                            |       10        20        30        40        50        
                            |                                                         
                            1-MSE                                                     


Chain B from PDB  Type:PROTEIN  Length:57
 aligned with Y1088_NEIMB | Q7DDI1 from UniProtKB/Swiss-Prot  Length:56

    Alignment length:57
                                                                                  56 
                                    10        20        30        40        50     | 
           Y1088_NEIMB    1 MYFEIYKDAKGEYRWRLKAANHEIIAQGEGYTSKQNCQHAVDLLKSTTAATPVKEV-  -
               SCOP domains d3bidb_ B: Uncharacterized protein NMB1088                SCOP domains
               CATH domains -3bidB01 B:2-47 YegP-like domains              ---------- CATH domains
               Pfam domains --------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.....eeeeee.....eeee.....hhhhhhhhhhhhhh......eeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------- Transcript
                  3bid B  1 mYFEIYKDAKGEYRWRLKAANHEIIAQGEGYTSKQNCQHAVDLLKSTTAATPVKEVL 57
                            |       10        20        30        40        50       
                            1-MSE                                                    


Chain C from PDB  Type:PROTEIN  Length:58
 aligned with Y1088_NEIMB | Q7DDI1 from UniProtKB/Swiss-Prot  Length:56

    Alignment length:58
                                                                                  56  
                                    10        20        30        40        50     |  
           Y1088_NEIMB    1 MYFEIYKDAKGEYRWRLKAANHEIIAQGEGYTSKQNCQHAVDLLKSTTAATPVKEV--  -
               SCOP domains d3bidc_ C: Uncharacterized protein NMB1088                 SCOP domains
               CATH domains -3bidC01 C:2-47 YegP-like domains              ----------- CATH domains
               Pfam domains ---------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.....eeeeee.....eeee.....hhhhhhhhhhhhhh......eee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------- Transcript
                  3bid C  1 mYFEIYKDAKGEYRWRLKAANHEIIAQGEGYTSKQNCQHAVDLLKSTTAATPVKEVLE 58
                            |       10        20        30        40        50        
                            1-MSE                                                     


Chain D from PDB  Type:PROTEIN  Length:57
 aligned with Y1088_NEIMB | Q7DDI1 from UniProtKB/Swiss-Prot  Length:56

    Alignment length:57
                                                                                  56 
                                    10        20        30        40        50     | 
           Y1088_NEIMB    1 MYFEIYKDAKGEYRWRLKAANHEIIAQGEGYTSKQNCQHAVDLLKSTTAATPVKEV-  -
               SCOP domains d3bidd_ D: Uncharacterized protein NMB1088                SCOP domains
               CATH domains -3bidD01 D:2-47 YegP-like domains              ---------- CATH domains
               Pfam domains --------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.....eeeeee.....eeeeeeee.hhhhhhhhhhhhhh......eee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------- Transcript
                  3bid D  1 mYFEIYKDAKGEYRWRLKAANHEIIAQGEGYTSKQNCQHAVDLLKSTTAATPVKEVL 57
                            |       10        20        30        40        50       
                            1-MSE                                                    


Chain E from PDB  Type:PROTEIN  Length:61
 aligned with Y1088_NEIMB | Q7DDI1 from UniProtKB/Swiss-Prot  Length:56

    Alignment length:61
                                                                                  56     
                                    10        20        30        40        50     |   - 
           Y1088_NEIMB    1 MYFEIYKDAKGEYRWRLKAANHEIIAQGEGYTSKQNCQHAVDLLKSTTAATPVKEV-----  -
               SCOP domains d3bide_ E: Uncharacterized protein NMB1088                    SCOP domains
               CATH domains -3bidE01 E:2-47 YegP-like domains              -------------- CATH domains
               Pfam domains ------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.....eeeeee.....eeee.....hhhhhhhhhhhhhh......eee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------- Transcript
                  3bid E  1 mYFEIYKDAKGEYRWRLKAANHEIIAQGEGYTSKQNCQHAVDLLKSTTAATPVKEVLEHHH 61
                            |       10        20        30        40        50        60 
                            1-MSE                                                        


Chain F from PDB  Type:PROTEIN  Length:58
 aligned with Y1088_NEIMB | Q7DDI1 from UniProtKB/Swiss-Prot  Length:56

    Alignment length:58
                                                                                  56  
                                    10        20        30        40        50     |  
           Y1088_NEIMB    1 MYFEIYKDAKGEYRWRLKAANHEIIAQGEGYTSKQNCQHAVDLLKSTTAATPVKEV--  -
               SCOP domains d3bidf_ F: Uncharacterized protein NMB1088                 SCOP domains
               CATH domains -3bidF01 F:2-47 YegP-like domains              ----------- CATH domains
               Pfam domains ---------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.....eeeeee.....eeee.....hhhhhhhhhhhhhh......eee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------- Transcript
                  3bid F  1 mYFEIYKDAKGEYRWRLKAANHEIIAQGEGYTSKQNCQHAVDLLKSTTAATPVKEVLE 58
                            |       10        20        30        40        50        
                            1-MSE                                                     


Chain G from PDB  Type:PROTEIN  Length:60
 aligned with Y1088_NEIMB | Q7DDI1 from UniProtKB/Swiss-Prot  Length:56

    Alignment length:60
                                                                                  56    
                                    10        20        30        40        50     |   -
           Y1088_NEIMB    1 MYFEIYKDAKGEYRWRLKAANHEIIAQGEGYTSKQNCQHAVDLLKSTTAATPVKEV----  -
               SCOP domains d3bidg_ G: Uncharacterized protein NMB1088                   SCOP domains
               CATH domains -3bidG01 G:2-47 YegP-like domains              ------------- CATH domains
               Pfam domains ------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeee.....eeeeee.....eeee.....hhhhhhhhhhhhhh......eee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------ Transcript
                  3bid G  1 mYFEIYKDAKGEYRWRLKAANHEIIAQGEGYTSKQNCQHAVDLLKSTTAATPVKEVLEHH 60
                            |       10        20        30        40        50        60
                            1-MSE                                                       


Chain H from PDB  Type:PROTEIN  Length:57
 aligned with Y1088_NEIMB | Q7DDI1 from UniProtKB/Swiss-Prot  Length:56

    Alignment length:57
                                                                                  56 
                                    10        20        30        40        50     | 
           Y1088_NEIMB    1 MYFEIYKDAKGEYRWRLKAANHEIIAQGEGYTSKQNCQHAVDLLKSTTAATPVKEV-  -
               SCOP domains d3bidh_ H: Uncharacterized protein NMB1088                SCOP domains
               CATH domains -3bidH01 H:2-47 YegP-like domains              ---------- CATH domains
               Pfam domains --------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.....eeeeee.....eeeeeeee.hhhhhhhhhhhhhh......eeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------- Transcript
                  3bid H  1 mYFEIYKDAKGEYRWRLKAANHEIIAQGEGYTSKQNCQHAVDLLKSTTAATPVKEVL 57
                            |       10        20        30        40        50       
                            1-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  (1, 8)

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

(-) CATH Domains  (1, 8)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

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

 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
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
(no "Sites" information available for 3bid)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3bid)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]
    Biological Unit 3  [ Jena3D ]
    Biological Unit 4  [ 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 | Biol. Unit 1 PNG format | Biol. Unit 2 PNG format | Biol. Unit 3 PNG format | Biol. Unit 4 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
  3bid
    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
  Y1088_NEIMB | Q7DDI1
    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)
  (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
  Y1088_NEIMB | Q7DDI1
    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 3BID)

(-) Related Entries Specified in the PDB File

mr91