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 :  DCMP HYDROXYMETHYLASE FROM T4
 
Authors :  H. K. Song, S. H. Sohn, S. W. Suh
Date :  06 Jan 99  (Deposition) - 13 Jan 99  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Biol. Unit 2:  A,B  (1x)
Keywords :  Hydroxymethylase, Dntp Synthesizing Complex, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. K. Song, S. H. Sohn, S. W. Suh
Crystal Structure Of Deoxycytidylate Hydroxymethylase From Bacteriophage T4, A Component Of The Deoxyribonucleoside Triphosphate-Synthesizing Complex.
Embo J. V. 18 1104 1999
PubMed-ID: 10064578  |  Reference-DOI: 10.1093/EMBOJ/18.5.1104

(-) Compounds

Molecule 1 - PROTEIN (DEOXYCYTIDYLATE HYDROXYMETHYLASE)
    Chains: A, B
    EC Number: 2.1.2.8
    Organism Scientific: ENTEROBACTERIA PHAGE T4
    Organism Taxid: 10665
    Synonym: DEOXYCYTIDYLATE HYDROXYMETHYLASE, DCMP HYDROXYMETHYLASE

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1DCM2Ligand/Ion2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1DCM4Ligand/Ion2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1DCM2Ligand/Ion2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:28 , TYR A:96 , CYS A:148 , ARG A:168 , SER A:169 , ASN A:170 , ASP A:171 , GLY A:175 , ASP A:179 , HIS A:216 , TYR A:218 , HOH A:303 , HOH A:315 , ARG B:123 , ARG B:124BINDING SITE FOR RESIDUE DCM A 300
2AC2SOFTWAREARG A:123 , ARG A:124 , LYS B:28 , TYR B:96 , CYS B:148 , ARG B:168 , SER B:169 , ASN B:170 , ASP B:171 , GLY B:175 , ASP B:179 , HIS B:216 , TYR B:218 , HOH B:401 , HOH B:403 , HOH B:415BINDING SITE FOR RESIDUE DCM B 400
3CATAUTHORCYS A:148 , CYS B:148THE SG ATOM OF CYS 148 HAS DUAL CONFORMATION

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1B5E)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1B5E)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1B5E)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1B5E)

(-) Exons   (0, 0)

(no "Exon" information available for 1B5E)

(-) 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:241
 aligned with DCHM_BPT4 | P08773 from UniProtKB/Swiss-Prot  Length:246

    Alignment length:241
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240 
            DCHM_BPT4     1 MISDSMTVEEIRLHLGLALKEKDFVVDKTGVKTIEIIGASFVADEPFIFGALNDEYIQRELEWYKSKSLFVKDIPGETPKIWQQVASSKGEINSNYGWAIWSEDNYAQYDMCLAELGQNPDSRRGIMIYTRPSMQFDYNKDGMSDFMCTNTVQYLIRDKKINAVVNMRSNDVVFGFRNDYAWQKYVLDKLVSDLNAGDSTRQYKAGSIIWNVGSLHVYSRHFYLVDHWWKTGETHISKKDY 241
               SCOP domains d1b5ea_ A: dCMP hydroxymethylase                                                                                                                                                                                                                  SCOP domains
               CATH domains 1b5eA00 A:1-241 Thymidylate Synthase, chain A                                                                                                                                                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhh............eeeee.eeee...........hhhhhhhhhhhhh....hhh......hhhhhh..........hhhhhh.hhh..hhhhhhhhhhh.......eee...hhhhhhhhhhh......eeeeeeeee..eeeeeeee.eee..hhhhhhhhhhhhhhhhhhhhhhhh..........eeeee.eeeeehhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1b5e A   1 MISDSMTVEEIRLHLGLALKEKDFVVDKTGVKTIEIIGASFVADEPFIFGALNDEYIQRELEWYKSKSLFVKDIPGETPKIWQQVASSKGEINSNYGWAIWSEDNYAQYDMCLAELGQNPDSRRGIMIYTRPSMQFDYNKDGMSDFMCTNTVQYLIRDKKINAVVNMRSNDVVFGFRNDYAWQKYVLDKLVSDLNAGDSTRQYKAGSIIWNVGSLHVYSRHFYLVDHWWKTGETHISKKDY 241
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240 


Chain B from PDB  Type:PROTEIN  Length:241
 aligned with DCHM_BPT4 | P08773 from UniProtKB/Swiss-Prot  Length:246

    Alignment length:241
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240 
            DCHM_BPT4     1 MISDSMTVEEIRLHLGLALKEKDFVVDKTGVKTIEIIGASFVADEPFIFGALNDEYIQRELEWYKSKSLFVKDIPGETPKIWQQVASSKGEINSNYGWAIWSEDNYAQYDMCLAELGQNPDSRRGIMIYTRPSMQFDYNKDGMSDFMCTNTVQYLIRDKKINAVVNMRSNDVVFGFRNDYAWQKYVLDKLVSDLNAGDSTRQYKAGSIIWNVGSLHVYSRHFYLVDHWWKTGETHISKKDY 241
               SCOP domains d1b5eb_ B: dCMP hydroxymethylase                                                                                                                                                                                                                  SCOP domains
               CATH domains 1b5eB00 B:1-241 Thymidylate Synthase, chain A                                                                                                                                                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhh............eeeee.eeee...........hhhhhhhhhhhhh....hhh......hhhh............hhhhhh.hhh..hhhhhhhhhhh.......eee...hhhhhhhhhhh......eeeeeeeee..eeeeeeee.eee..hhhhhhhhhhhhhhhhhhhhhhhh..........eeeee.eeeeehhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1b5e B   1 MISDSMTVEEIRLHLGLALKEKDFVVDKTGVKTIEIIGASFVADEPFIFGALNDEYIQRELEWYKSKSLFVKDIPGETPKIWQQVASSKGEINSNYGWAIWSEDNYAQYDMCLAELGQNPDSRRGIMIYTRPSMQFDYNKDGMSDFMCTNTVQYLIRDKKINAVVNMRSNDVVFGFRNDYAWQKYVLDKLVSDLNAGDSTRQYKAGSIIWNVGSLHVYSRHFYLVDHWWKTGETHISKKDY 241
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240
   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 Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1B5E)

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (DCHM_BPT4 | P08773)
molecular function
    GO:0047153    deoxycytidylate 5-hydroxymethyltransferase activity    Catalysis of the reaction: 5,10-methylenetetrahydrofolate + dCMP + H(2)O = (6S)-5,6,7,8-tetrahydrofolate + 5-hydroxymethyldeoxycytidylate.
    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.

 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
    DCM  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    CAT  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1b5e)
 
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
  1b5e
    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
  DCHM_BPT4 | P08773
    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)
  2.1.2.8
    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
  DCHM_BPT4 | P08773
    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
        DCHM_BPT4 | P08773: 1b49 1b5d

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1B5E)