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
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)

(-) Description

Title :  CRYSTAL STRUCTURE OF MLL3558 PROTEIN FROM RHIZOBIUM LOTI. NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET ID MLR403
 
Authors :  J. Seetharaman, Y. Chen, D Wang, C. Ciccosanti, S. Sahdev, B. Rost, T. B R. Xiao, J. K. Everett, G. T. Montelione, L. Tong, J. F. Hunt, Northeast Structural Genomics Consortium (Nesg)
Date :  01 Apr 11  (Deposition) - 25 May 11  (Release) - 25 May 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A (1x),B (1x)
Keywords :  Structural Genomics, Psi-Biology, Northeast Structural Genomics Consortium, Nesg, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Seetharaman, Y. Chen, D. Wang, C. Ciccosanti, S. Sahdev, B. Rost, T. B. Acton, R. Xiao, J. K. Everett, G. T. Montelione, L. Tong, J. F. Hunt Northeast Structural Genomics Consortium (Nesg)
Crystal Structure Of Mll3558 Protein From Rhizobium Loti. Northeast Structural Genomics Consortium Target Id Mlr403
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - MLL3558 PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: MLL3558
    Organism Scientific: MESORHIZOBIUM LOTI
    Organism Taxid: 381

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): AB
Biological Unit 2 (1x): A (1x)B (1x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 3RD6)

(-) Sites  (0, 0)

(no "Site" information available for 3RD6)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3RD6)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Gly B:94 -Pro B:95

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3RD6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3RD6)

(-) Exons   (0, 0)

(no "Exon" information available for 3RD6)

(-) 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:144
 aligned with Q98FZ2_RHILO | Q98FZ2 from UniProtKB/TrEMBL  Length:161

    Alignment length:147
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       
         Q98FZ2_RHILO    11 HSVIHSTFTIERTYPQSPDRVFHAFADKATVRRWRVDGDGFTVAEFSFDFRVGGGEVSRFSYGGGPEVRLDAQFQDIVPDQRIVFSYRMAIGPQPMSASLTTVELTPSGDGTRLTYTEQGAFFDGVDSAKGREEGTRGLLEALAAEL 157
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeeee..hhhhhhhhhhhhhhhhhhh.....---.eeee......eeeeee.......eeeeeeeeeee...eeeeeeeeee..eeeeeeeeeeeeeee..eeeeeeeeeeeee....hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3rd6 A   3 HSVIHSTFTIERTYPQSPDRVFHAFADKATVRRWRVDGDG---AEFSFDFRVGGGEVSRFSYGGGPEVRLDAQFQDIVPDQRIVFSYRMAIGPQPMSASLTTVELTPSGDGTRLTYTEQGAFFDGVDSAKGREEGTRGLLEALAAEL 149
                                    12        22        32        42   |    52        62        72        82        92       102       112       122       132       142       
                                                                  42  46                                                                                                       


Chain B from PDB  Type:PROTEIN  Length:135
 aligned with Q98FZ2_RHILO | Q98FZ2 from UniProtKB/TrEMBL  Length:161

    Alignment length:150
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160
         Q98FZ2_RHILO    11 HSVIHSTFTIERTYPQSPDRVFHAFADKATVRRWRVDGDGFTVAEFSFDFRVGGGEVSRFSYGGGPEVRLDAQFQDIVPDQRIVFSYRMAIGPQPMSASLTTVELTPSGDGTRLTYTEQGAFFDGVDSAKGREEGTRGLLEALAAELQKW 160
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) --------------AHSA1-3rd6B01 B:17-150                                                                                                                -- Pfam domains (1)
           Pfam domains (2) --------------AHSA1-3rd6B02 B:17-150                                                                                                                -- Pfam domains (2)
         Sec.struct. author ...eeeeeeeeee...hhhhhhhhhhhhhhhhhh..----.................eeee.....eeeeeeeeeeee...eeeeeeeee....eeeeeeeeeeee.----.eeeeeeeeee.-------hhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3rd6 B   3 HSVIHSTFTIERTYPQSPDRVFHAFADKATVRRWRV----FTVAEFSFDFRVGGGEVSRFSYGGGPEVRLDAQFQDIVPDQRIVFSYRMAIGPQPMSASLTTVELTP----TRLTYTEQGAFF-------GREEGTRGLLEALAAELQKW 152
                                    12        22        32     |   -|       52        62        72        82        92       102      |  - |     122  |      -|      142       152
                                                              38   43                                                               109  114        125     133
   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 3RD6)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3RD6)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: Bet_V_1_like (93)

(-) Gene Ontology  (1, 1)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q98FZ2_RHILO | Q98FZ2)
biological process
    GO:0006950    response to stress    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a disturbance in organismal or cellular homeostasis, usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation).

 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
(no "Ligands, Modified Residues, Ions" information available for 3rd6)
 
  Sites
(no "Sites" information available for 3rd6)
 
  Cis Peptide Bonds
    Gly B:94 - Pro B:95   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ 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 ](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
  3rd6
    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
  Q98FZ2_RHILO | Q98FZ2
    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
  Q98FZ2_RHILO | Q98FZ2
    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 3RD6)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3RD6)