Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
(-)Biological Unit 3
(-)Biological Unit 4
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (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 E. COLI DNA ADENINE METHYLTRANSFERASE IN COMPLEX WITH BENZOTHIOPHENE AZA-SAM
 
Authors :  J. E. Harmer, P. L. Roach
Date :  20 Aug 12  (Deposition) - 26 Feb 14  (Release) - 26 Feb 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  D,E,F
Biol. Unit 1:  D,E,F  (1x)
Biol. Unit 2:  D  (1x)
Biol. Unit 3:  E  (1x)
Biol. Unit 4:  F  (1x)
Keywords :  Transferase, Methylation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. E. Harmer, J. C. Mckelvie, G. Hobley, P. L. Roach
Structural Basis Of Selective N-6 Adenine Methyltransferase Inhibition By Transition State Mimic
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - DNA ADENINE METHYLASE
    Chains: D, E, F
    EC Number: 2.1.1.72
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET24D
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: B3387, DAM, JW3350
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K-12
    Synonym: DNA ADENINE METHYLTRANSFERASE, DEOXYADENOSYL- METHYLTRANSFERASE, M.ECODAM

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : DEF
Biological Unit 1 (1x): DEF
Biological Unit 2 (1x): D  
Biological Unit 3 (1x):  E 
Biological Unit 4 (1x):   F

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric Unit (1, 3)
No.NameCountTypeFull Name
10Y23Ligand/Ion5'-{[(3S)-3-AMINO-3-CARBOXYPROPYL][2-(1-BENZOTHIOPHEN-3-YL)ETHYL]AMINO}-5'-DEOXYADENOSINE
Biological Unit 1 (1, 3)
No.NameCountTypeFull Name
10Y23Ligand/Ion5'-{[(3S)-3-AMINO-3-CARBOXYPROPYL][2-(1-BENZOTHIOPHEN-3-YL)ETHYL]AMINO}-5'-DEOXYADENOSINE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
10Y21Ligand/Ion5'-{[(3S)-3-AMINO-3-CARBOXYPROPYL][2-(1-BENZOTHIOPHEN-3-YL)ETHYL]AMINO}-5'-DEOXYADENOSINE
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
10Y21Ligand/Ion5'-{[(3S)-3-AMINO-3-CARBOXYPROPYL][2-(1-BENZOTHIOPHEN-3-YL)ETHYL]AMINO}-5'-DEOXYADENOSINE
Biological Unit 4 (1, 1)
No.NameCountTypeFull Name
10Y21Ligand/Ion5'-{[(3S)-3-AMINO-3-CARBOXYPROPYL][2-(1-BENZOTHIOPHEN-3-YL)ETHYL]AMINO}-5'-DEOXYADENOSINE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS D:9 , TRP D:10 , PRO D:34 , PHE D:35 , ASP D:54 , ILE D:55 , SER D:164 , TYR D:165 , ASP D:181 , PRO D:182 , PRO D:183 , TYR D:184BINDING SITE FOR RESIDUE 0Y2 D 301
2AC2SOFTWAREALA E:11 , PRO E:34 , PHE E:35 , ALA E:38 , ASP E:54 , ILE E:55 , CYS E:123 , SER E:164 , TYR E:165 , ASP E:181 , PRO E:182 , PRO E:183 , TYR E:184BINDING SITE FOR RESIDUE 0Y2 E 301
3AC3SOFTWARELYS F:9 , TRP F:10 , PRO F:34 , PHE F:35 , ALA F:38 , ASP F:54 , ILE F:55 , SER F:164 , TYR F:165 , ASP F:181 , PRO F:182 , PRO F:183 , TYR F:184BINDING SITE FOR RESIDUE 0Y2 F 301

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4GOO)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Trp D:10 -Ala D:11
2Gly D:12 -Gly D:13
3Gly D:13 -Lys D:14

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4GOO)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4GOO)

(-) Exons   (0, 0)

(no "Exon" information available for 4GOO)

(-) 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 D from PDB  Type:PROTEIN  Length:243
                                                                                                                                                                                                                                                                                   
               SCOP domains d4good_ D: automated matches                                                                                                                                                                                                                        SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............hhhhhhhhh....eeee.......hhhhh...eeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh.....................hhhhhhhhhhhh..eeeee.hhhhhhh.....eeeee..........hhhhhhhhhhhhhhhhhh...eeeeee.hhhhhhhh...eeeee...eeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4goo D   3 KNRAFLKWAGGKYPLLDDIKRHLPKGECLVEPFVGAGSVFLNTDFSRYILADINSDLISLYNIVKMRTDEYVQAARELFVPETNCAEVYYQFREEFNKSQDPFRRAVLFLYLNRYGYNGLCRYNLRGEFNVPFGRYKKPYFPEAELYHFAEKAQNAFFYCESYADSMARADDASVVYCDPPYAPLNSFTLEQQAHLAEIAEGLVERHIPVLISNHDTMLTREWYQRAKLHVVKVDELLALYKP 270
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182    || 203       213       223       233       243  ||   267   
                                                                                                                                                                                                                  187|                                            246|         
                                                                                                                                                                                                                   199                                             261         


Chain E from PDB  Type:PROTEIN  Length:244
                                                                                                                                                                                                                                                                                    
               SCOP domains d4gooe_ E: automated matches                                                                                                                                                                                                                         SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............hhhhhhhhh....eeee.....hhhhhh....eeeeee.hhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh.....................hhhhhhhhhhhh..eeeee.hhhhhhh.....eeeee.........hhhhhhhhhhhhhhhhhh...eeeeee.hhhhhhhh...eeeee.....eeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4goo E   3 KNRAFLKWAGGKYPLLDDIKRHLPKGECLVEPFVGAGSVFLNTDFSRYILADINSDLISLYNIVKMRTDEYVQAARELFVPETNCAEVYYQFREEFNKSQDPFRRAVLFLYLNRYGYNGLCRYNLRGEFNVPFGRYKKPYFPEAELYHFAEKAQNAFFYCESYADSMARADDASVVYCDPPYAPLSFTLEQQAHLAEIAEGLVERHIPVLISNHDTMLTREWYQRAKLHVVKVKVDELLALYKP 270
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182    || 204       214       224       234       244  ||   266    
                                                                                                                                                                                                                  187|                                            247|          
                                                                                                                                                                                                                   200                                             260          


Chain F from PDB  Type:PROTEIN  Length:244
                                                                                                                                                                                                                                                                                    
               SCOP domains d4goof_ F: automated matches                                                                                                                                                                                                                         SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............hhhhhhhhh....eeee.....hhhhhh....eeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh.....................hhhhhhhhhhhhh.eeee..hhhhhhhh....eeeee..........hhhhhhhhhhhhhhhhh....eeeeee.hhhhhhhh...eeeee....eeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4goo F   3 KNRAFLKWAGGKYPLLDDIKRHLPKGECLVEPFVGAGSVFLNTDFSRYILADINSDLISLYNIVKMRTDEYVQAARELFVPETNCAEVYYQFREEFNKSQDPFRRAVLFLYLNRYGYNGLCRYNLRGEFNVPFGRYKKPYFPEAELYHFAEKAQNAFFYCESYADSMARADDASVVYCDPPYAPLNSFTLEQQAHLAEIAEGLVERHIPVLISNHDTMLTREWYQRAKLHVVKVVDELLALYKP 270
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182    || 203       213       223       233       243   ||  266    
                                                                                                                                                                                                                  187|                                             247|         
                                                                                                                                                                                                                   199                                              261
   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, 3)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4GOO)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4GOO)

(-) Gene Ontology  (12, 12)

Asymmetric Unit(hide GO term definitions)

 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
    0Y2  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Gly D:12 - Gly D:13   [ RasMol ]  
    Gly D:13 - Lys D:14   [ RasMol ]  
    Trp D:10 - Ala D:11   [ RasMol ]  
 
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 | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites 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
  4goo
    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
  DMA_ECOLI | P0AEE8
    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)
  2.1.1.72
    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
  DMA_ECOLI | P0AEE8
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        DMA_ECOLI | P0AEE8: 2g1p 2ore 4gbe 4gol 4gom 4gon 4rtj 4rtk 4rtl 4rtm 4rtn 4rto 4rtp 4rtq 4rtr 4rts

(-) Related Entries Specified in the PDB File

4gbe 4gol 4gom 4gon