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 :  CRYSTAL STRUCTURE OF APC86534.1 (C-TERMINAL DOMAIN OF NCBI AAB90184.1; PFAM BIG 123.1)
 
Authors :  A. Joachimiak, N. Duke, M. Zhou, M. Gu, Midwest Center For Structural Genomics (Mcsg)
Date :  16 Jul 07  (Deposition) - 14 Aug 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Alpha/Beta Knot, Sam, Structural Genomics, Psi-2, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Joachimiak, N. Duke, M. Zhou, M. Gu
Crystal Structure Of Apc86534. 1 (C-Terminal Domain Of Ncbi Aab90184. 1; Pfam Big 123. 1).
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - UPF0217 PROTEIN AF_1056
    Atcc: 49558
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG7
    Expression System Strain: BL21 MAGIC
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: AF_1056
    Organism Scientific: ARCHAEOGLOBUS FULGIDUS DSM 4304
    Organism Taxid: 224325
    Strain: DSM 4304, VC-16, JCM 9628, NBRC 100126

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1SAM2Ligand/IonS-ADENOSYLMETHIONINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:221 , LYS A:222 , GLU A:223 , GLY A:242 , ASP A:243 , GLY A:246 , SER A:264 , LEU A:265 , SER A:266 , LEU A:268 , SER A:269 , LEU A:270 , CYS A:275 , HOH A:337BINDING SITE FOR RESIDUE SAM A 301
2AC2SOFTWARELEU B:221 , LYS B:222 , GLU B:223 , ILE B:241 , GLY B:242 , ASP B:243 , GLY B:246 , LEU B:263 , SER B:264 , LEU B:265 , SER B:266 , LEU B:268 , SER B:269 , LEU B:270 , CYS B:275 , HOH B:329 , HOH B:349BINDING SITE FOR RESIDUE SAM B 301

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2QMM)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Pro A:151 -Pro A:152
2Pro A:154 -Pro A:155
3Pro B:151 -Pro B:152
4Pro B:154 -Pro B:155

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2QMM)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2QMM)

(-) Exons   (0, 0)

(no "Exon" information available for 2QMM)

(-) 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:195
 aligned with TRMY_ARCFU | O29206 from UniProtKB/Swiss-Prot  Length:288

    Alignment length:195
                                   103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283     
           TRMY_ARCFU    94 VVRGFLIVGNKAFTQPFSLNDLPGAGRMDVLCRCTSQALFISHGIRRDVEVYLLLLGPPSPPKSILIKGDEVRRMSPDERNVAGHIKKALAVECGKSWKKVHSGVYVSRKGLEELIEELSEKYSIIYLKEDGVDISNAQLPPNPLFVIGDHEGLTEEQEKVVERYAALKLSLSPLSLLAEQCVVIAHHHLDRLQF 288
               SCOP domains -d2qmma1 A:95-288 Uncharacterized protein AF1056                                                                                                                                                    SCOP domains
               CATH domains 2qmmA00 A:94-288  [code=3.40.1280.10, no name defined]                                                                                                                                              CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee.................hhhhhhhhhhhhhee..ee...eeeeeee.......eeeeee.........hhhhhhhhhhhhhhh......eeee..eeee..hhhhhhhhhhhhheeeee....ee.hhh.....eeeeee.....hhhhhhhhhh...eeee......hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qmm A  94 AVRGFLIVGNKAFTQPFSLNDLPGAGRMDVLCRCTSQALFISHGIRRDVEVYLLLLGPPSPPKSILIKGDEVRRMSPDERNVAGHIKKALAVECGKSWKKVHSGVYVSRKGLEELIEELSEKYSIIYLKEDGVDISNAQLPPNPLFVIGDHEGLTEEQEKVVERYAALKLSLSPLSLLAEQCVVIAHHHLDRLQF 288
                                   103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283     


Chain B from PDB  Type:PROTEIN  Length:195
 aligned with TRMY_ARCFU | O29206 from UniProtKB/Swiss-Prot  Length:288

    Alignment length:195
                                   103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283     
           TRMY_ARCFU    94 VVRGFLIVGNKAFTQPFSLNDLPGAGRMDVLCRCTSQALFISHGIRRDVEVYLLLLGPPSPPKSILIKGDEVRRMSPDERNVAGHIKKALAVECGKSWKKVHSGVYVSRKGLEELIEELSEKYSIIYLKEDGVDISNAQLPPNPLFVIGDHEGLTEEQEKVVERYAALKLSLSPLSLLAEQCVVIAHHHLDRLQF 288
               SCOP domains d2qmmb_ B: Uncharacterized protein AF1056                                                                                                                                                           SCOP domains
               CATH domains 2qmmB00 B:94-288  [code=3.40.1280.10, no name defined]                                                                                                                                              CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee.................hhhhhhhhhhhhhee..ee...eeeeeee.......eeeeee.........hhhhhhhhhhhhhhh......eeee..eeee..hhhhhhhhhhh..eeeee....ee.hhh.....eeeeee.....hhhhhhhhhh...eeee......hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qmm B  94 AVRGFLIVGNKAFTQPFSLNDLPGAGRMDVLCRCTSQALFISHGIRRDVEVYLLLLGPPSPPKSILIKGDEVRRMSPDERNVAGHIKKALAVECGKSWKKVHSGVYVSRKGLEELIEELSEKYSIIYLKEDGVDISNAQLPPNPLFVIGDHEGLTEEQEKVVERYAALKLSLSPLSLLAEQCVVIAHHHLDRLQF 288
                                   103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283
   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, 2)

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

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2QMM)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (TRMY_ARCFU | O29206)
molecular function
    GO:0008757    S-adenosylmethionine-dependent methyltransferase activity    Catalysis of the transfer of a methyl group from S-adenosyl-L-methionine to a substrate.
    GO:0008168    methyltransferase activity    Catalysis of the transfer of a methyl group to an acceptor molecule.
    GO:0008175    tRNA methyltransferase activity    Catalysis of the transfer of a methyl group from a donor to a nucleoside residue in a tRNA molecule.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0032259    methylation    The process in which a methyl group is covalently attached to a molecule.
    GO:0030488    tRNA methylation    The posttranscriptional addition of methyl groups to specific residues in a tRNA molecule.
    GO:0008033    tRNA processing    The process in which a pre-tRNA molecule is converted to a mature tRNA, ready for addition of an aminoacyl group.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

 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
    SAM  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Pro A:151 - Pro A:152   [ RasMol ]  
    Pro A:154 - Pro A:155   [ RasMol ]  
    Pro B:151 - Pro B:152   [ RasMol ]  
    Pro B:154 - Pro B:155   [ RasMol ]  
 

(-) 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
  2qmm
    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
  TRMY_ARCFU | O29206
    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
  TRMY_ARCFU | O29206
    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 2QMM)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2QMM)