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
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)

(-) Description

Title :  CRYSTAL STRUCTURE OF ESCHERICHIA COLI YDCF, AN S-ADENOSYL-L-METHIONINE UTILIZING ENZYME
 
Authors :  K. Lim, K. Chao, C. Lehmann, O. Herzberg, Structure 2 Function Proje
Date :  19 Feb 08  (Deposition) - 06 May 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Two Domains, Alpha/Beta Fold, Helix Bundle, Structural Genomics, Structure 2 Function Project, S2F, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. L. Chao, K. Lim, C. Lehmann, V. Doseeva, A. J. Howard, F. P. Schwarz, O. Herzberg
The Escherichia Coli Ydcf Binds S-Adenosyl-L-Methionine And Adopts An Alpha/Beta-Fold Characteristic Of Nucleotide-Utilizing Enzymes.
Proteins V. 72 506 2008
PubMed-ID: 18393394  |  Reference-DOI: 10.1002/PROT.22046

(-) Compounds

Molecule 1 - PROTEIN YDCF
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET100/D-TOPO
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: YDCF, B1414, JW1411
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K12

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 22)

Asymmetric Unit (2, 22)
No.NameCountTypeFull Name
1MPD14Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
2SO48Ligand/IonSULFATE ION
Biological Unit 1 (2, 11)
No.NameCountTypeFull Name
1MPD7Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
2SO44Ligand/IonSULFATE ION
Biological Unit 2 (2, 11)
No.NameCountTypeFull Name
1MPD7Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
2SO44Ligand/IonSULFATE ION

(-) Sites  (22, 22)

Asymmetric Unit (22, 22)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:92 , ARG A:96 , HOH A:1457BINDING SITE FOR RESIDUE SO4 A 801
02AC2SOFTWAREHIS A:73 , ASN A:125 , CYS A:126 , ARG A:158 , HOH A:1025 , HOH A:1256 , HOH A:1267 , HOH A:1572BINDING SITE FOR RESIDUE SO4 A 802
03AC3SOFTWAREARG B:96 , THR B:100 , HOH B:1085 , HOH B:1482BINDING SITE FOR RESIDUE SO4 B 803
04AC4SOFTWAREHIS B:73 , ASN B:125 , CYS B:126 , ARG B:158 , HOH B:1402 , HOH B:1514BINDING SITE FOR RESIDUE SO4 B 804
05AC5SOFTWAREARG A:220 , LYS A:251 , HOH A:1661 , HOH A:1672BINDING SITE FOR RESIDUE SO4 A 805
06AC6SOFTWAREARG B:220 , LYS B:251 , HOH B:1416 , HOH B:1481 , HOH B:1626BINDING SITE FOR RESIDUE SO4 B 806
07AC7SOFTWAREASP A:222 , SER A:223 , ARG A:229 , HOH A:1455BINDING SITE FOR RESIDUE SO4 A 807
08AC8SOFTWAREASP B:222 , SER B:223 , ARG B:229BINDING SITE FOR RESIDUE SO4 B 808
09AC9SOFTWAREPRO A:49 , ASP A:52 , GLY A:181 , HOH A:1017 , HOH A:1105 , HOH A:1249BINDING SITE FOR RESIDUE MPD A 901
10BC1SOFTWAREPHE A:77 , SER A:80 , TRP A:203 , PRO A:204 , HOH A:1002 , HOH A:1515BINDING SITE FOR RESIDUE MPD A 902
11BC2SOFTWAREARG A:131 , ILE A:134 , MET A:166 , HOH A:1656 , HOH B:1004 , HOH B:1214BINDING SITE FOR RESIDUE MPD A 903
12BC3SOFTWAREPRO B:49 , ASP B:52 , ALA B:53 , GLY B:181 , HOH B:1053 , HOH B:1095BINDING SITE FOR RESIDUE MPD B 904
13BC4SOFTWAREALA B:46 , PHE B:77 , SER B:80 , GLN B:84 , TRP B:203 , PRO B:204 , HOH B:1007BINDING SITE FOR RESIDUE MPD B 905
14BC5SOFTWAREHOH A:1010 , HOH A:1523 , ARG B:131 , MET B:166 , HOH B:1385BINDING SITE FOR RESIDUE MPD B 906
15BC6SOFTWAREHOH A:1106 , HOH A:1419 , HOH A:1512 , ASN B:125 , GLY B:127 , GLU B:128 , MET B:166 , HOH B:1509BINDING SITE FOR RESIDUE MPD A 907
16BC7SOFTWAREHIS A:87 , TYR A:88 , PHE A:109 , TRP A:110 , HOH A:1490BINDING SITE FOR RESIDUE MPD A 908
17BC8SOFTWARELEU A:137 , VAL A:144 , HIS A:145 , ARG A:175BINDING SITE FOR RESIDUE MPD A 909
18BC9SOFTWAREPRO B:34 , TYR B:35 , ALA B:83 , HOH B:1045 , HOH B:1181 , HOH B:1545BINDING SITE FOR RESIDUE MPD B 910
19CC1SOFTWAREGLN B:36 , ALA B:37 , ASP B:38 , THR B:94 , THR B:146 , HOH B:1119 , HOH B:1178 , HOH B:1333BINDING SITE FOR RESIDUE MPD B 911
20CC2SOFTWAREPHE A:132 , ALA A:135 , LEU B:136 , GLN B:139 , HOH B:1143 , HOH B:1546 , HOH B:1557BINDING SITE FOR RESIDUE MPD A 912
21CC3SOFTWARETYR B:88 , PHE B:109 , TRP B:110 , HOH B:1562BINDING SITE FOR RESIDUE MPD B 913
22CC4SOFTWAREGLN B:108 , PHE B:109 , HOH B:1039 , HOH B:1120 , HOH B:1582BINDING SITE FOR RESIDUE MPD B 914

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3CA8)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3CA8)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3CA8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3CA8)

(-) Exons   (0, 0)

(no "Exon" information available for 3CA8)

(-) 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:261
 aligned with YDCF_ECOLI | P34209 from UniProtKB/Swiss-Prot  Length:266

    Alignment length:261
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264 
           YDCF_ECOLI     5 PFPTLSPATIDAINVIGQWLAQDDFSGEVPYQADCVILAGNAVMPTIDAACKIARDQQIPLLISGGIGHSTTFLYSAIAQHPHYNTIRTTGRAEATILADIAHQFWHIPHEKIWIEDQSTNCGENARFSIALLNQAVERVHTAIVVQDPTMQRRTMATFRRMTGDNPDAPRWLSYPGFVPQLGNNADSVIFINQLQGLWPVERYLSLLTGELPRLRDDSDGYGPRGRDFIVHVDFPAEVIHAWQTLKHDAVLIEAMESRSL 265
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3ca8A01               3ca8A02 A:27-181 Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1                                                                                     3ca8A01 A:5-26,A:182-265 YdcF like domain                                            CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhh............eeeee...hhhhhhhhhhhhhhhh..eeee.....hhhhhhhhhhh..hhhhh.....hhhhhhhhhhhhh...hhh.eeee....hhhhhhhhhhhhhhh.......eeee....hhhhhhhhhhhhhh.......eee.......eeee..eeee........hhhhhhhhhhhhhhhhh...................hhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ca8 A   5 PFPTLSPATIDAINVIGQWLAQDDFSGEVPYQADCVILAGNAVMPTIDAACKIARDQQIPLLISGGIGHSTTFLYSAIAQHPHYNTIRTTGRAEATILADIAHQFWHIPHEKIWIEDQSTNCGENARFSIALLNQAVERVHTAIVVQDPTMQRRTMATFRRMTGDNPDAPRWLSYPGFVPQLGNNADSVIFINQLQGLWPVERYLSLLTGELPRLRDDSDGYGPRGRDFIVHVDFPAEVIHAWQTLKHDAVLIEAMESRSL 265
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264 


Chain B from PDB  Type:PROTEIN  Length:259
 aligned with YDCF_ECOLI | P34209 from UniProtKB/Swiss-Prot  Length:266

    Alignment length:259
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254         
           YDCF_ECOLI     5 PFPTLSPATIDAINVIGQWLAQDDFSGEVPYQADCVILAGNAVMPTIDAACKIARDQQIPLLISGGIGHSTTFLYSAIAQHPHYNTIRTTGRAEATILADIAHQFWHIPHEKIWIEDQSTNCGENARFSIALLNQAVERVHTAIVVQDPTMQRRTMATFRRMTGDNPDAPRWLSYPGFVPQLGNNADSVIFINQLQGLWPVERYLSLLTGELPRLRDDSDGYGPRGRDFIVHVDFPAEVIHAWQTLKHDAVLIEAMESR 263
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3ca8B01               3ca8B02 B:27-181 Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1                                                                                     3ca8B01 B:5-26,B:182-263 YdcF like domain                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhh............eeeee...hhhhhhhhhhhhhhhh..eeee.....hhhhhhhhhhh..hhhhh.....hhhhhhhhhhhhh...hhh.eeee....hhhhhhhhhhhhhhh.......eeee.hhhhhhhhhhhhhhhhh.......eee.......eeee..eeee........hhhhhhhhhhhhhhhhh...................hhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ca8 B   5 PFPTLSPATIDAINVIGQWLAQDDFSGEVPYQADCVILAGNAVMPTIDAACKIARDQQIPLLISGGIGHSTTFLYSAIAQHPHYNTIRTTGRAEATILADIAHQFWHIPHEKIWIEDQSTNCGENARFSIALLNQAVERVHTAIVVQDPTMQRRTMATFRRMTGDNPDAPRWLSYPGFVPQLGNNADSVIFINQLQGLWPVERYLSLLTGELPRLRDDSDGYGPRGRDFIVHVDFPAEVIHAWQTLKHDAVLIEAMESR 263
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254
   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 3CA8)

(-) CATH Domains  (2, 4)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3CA8)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3CA8)

 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
    MPD  [ 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 ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    BC1  [ RasMol ]  +environment [ RasMol ]
    BC2  [ RasMol ]  +environment [ RasMol ]
    BC3  [ RasMol ]  +environment [ RasMol ]
    BC4  [ RasMol ]  +environment [ RasMol ]
    BC5  [ RasMol ]  +environment [ RasMol ]
    BC6  [ RasMol ]  +environment [ RasMol ]
    BC7  [ RasMol ]  +environment [ RasMol ]
    BC8  [ RasMol ]  +environment [ RasMol ]
    BC9  [ RasMol ]  +environment [ RasMol ]
    CC1  [ RasMol ]  +environment [ RasMol ]
    CC2  [ RasMol ]  +environment [ RasMol ]
    CC3  [ RasMol ]  +environment [ RasMol ]
    CC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3ca8)
 
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 | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites 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
  3ca8
    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
  YDCF_ECOLI | P34209
    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
  YDCF_ECOLI | P34209
    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 3CA8)

(-) Related Entries Specified in the PDB File

ydcf