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(-) Description

Authors :  S. B. Renwick, K. Snell
Date :  02 Jul 98  (Deposition) - 16 Aug 99  (Release) - 13 Jul 11  (Revision)
Resolution :  2.65
Chains :  Asym./Biol. Unit :  A
Keywords :  Transferase, Metabolic Role, Pyridoxal 5'-Phosphate (Keyword Search: [Gene Ontology, PubMed, Web (Google))
Reference :  S. B. Renwick, K. Snell, U. Baumann
The Crystal Structure Of Human Cytosolic Serine Hydroxymethyltransferase: A Target For Cancer Chemotherapy
Structure V. 6 1105 1998
PubMed-ID: 9753690  |  Reference-DOI: 10.1016/S0969-2126(98)00112-9

(-) Compounds

    EC Number2.1.2.1
    Expression SystemESCHERICHIA COLI
    Expression System Cellular LocationCYTOPLASM
    Expression System GeneGLYC_HUMAN
    Expression System PlasmidPET-14B
    Expression System StrainBL21(DE3)PLYSS
    Expression System Taxid562
    Expression System VectorE.COLI
    Expression System Vector TypeT7 EXPRESSION VECTOR
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
1AC1SOFTWARETYR A:73 , SER A:119 , GLY A:120 , SER A:121 , HIS A:148 , THR A:202 , ASP A:228 , ALA A:230 , HIS A:231 , THR A:254 , HIS A:256 , LYS A:257 , GLY A:302 , GLY A:303BINDING SITE FOR RESIDUE PLP A 500

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1BJ4)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
1Phe A:297 -Pro A:298

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 2)

Asymmetric/Biological Unit (2, 2)
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
1SHMTPS00096 Serine hydroxymethyltransferase pyridoxal-phosphate attachment site.GLYC_HUMAN249-265  1A:249-265

(-) Exons   (11, 11)

Asymmetric/Biological Unit (11, 11)
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength

(-) 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:470
 aligned with GLYC_HUMAN | P34896 from UniProtKB/Swiss-Prot  Length:483

    Alignment length:470
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480
               SCOP domains d1bj4a_ A: Serine hydroxymethyltransferase                                                                                                                                                                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains -----------------------------------------------1bj4A01 A:58-320 Type I PLP-dependent aspartate aminotransferase-like (Major domain)                                                                                                                                                                                   1bj4A02 A:321-480 Aspartate Aminotransferase, domain 1                                                                                                           CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhh....hhhh.hhhhhhhhhhhhhhhh............hhhhhhhh.hhh................hhhhhhhhhhhhhhhhh.......eeee.....hhhhhhhhhhhh.....eeeee.hhh...hhh..........hhhhh.eeeee..........hhhhhhhhhhh...eeee..........hhhhhhhhhhh..eeeee.hhhhhhhh......hhh...eeeee..hhh.....eeeeee..eeee......eee..hhhhhhhhh.........hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh.............eeeeehhhh...hhhhhhhhhhh....eee............eeeee.hhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhh.....hhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Q-------------------------------------------------------------------------------------------------------------------------------------F------ SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------SHMT             ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2  PDB: A:11-32Exon 1.3a  PDB: A:33-81 UniProt: 33-81           --------------------------------------Exon 1.9  PDB: A:120-173 UniProt: 120-173             Exon 1.10b  PDB: A:174-201  ----------------------------------------------------------------------Exon 1.12  PDB: A:272-311               ----------------------------------------Exon 1.14  PDB: A:352-391               ------------------------------------Exon 1.16d  PDB: A:428-480 UniProt: 428-483           Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------------------Exon 1.8b  PDB: A:81-120 UniProt: 81-120--------------------------------------------------------------------------------Exon 1.11  PDB: A:201-272 UniProt: 201-272                              --------------------------------------Exon 1.13  PDB: A:311-352 UniProt: 311-352--------------------------------------Exon 1.15  PDB: A:391-428             ---------------------------------------------------- Transcript 1 (2)
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480

   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, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (2, 2)

Asymmetric/Biological Unit
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1BJ4)

(-) Gene Ontology  (30, 30)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (GLYC_HUMAN | P34896)
molecular function
    GO:0008732    L-allo-threonine aldolase activity    Catalysis of the reaction: L-allo-threonine = glycine + acetaldehyde.
    GO:0016597    amino acid binding    Interacting selectively and non-covalently with an amino acid, organic acids containing one or more amino substituents.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0004372    glycine hydroxymethyltransferase activity    Catalysis of the reaction: 5,10-methylenetetrahydrofolate + glycine + H2O = tetrahydrofolate + L-serine.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
    GO:0030170    pyridoxal phosphate binding    Interacting selectively and non-covalently with pyridoxal 5' phosphate, 3-hydroxy-5-(hydroxymethyl)-2-methyl4-pyridine carboxaldehyde 5' phosphate, the biologically active form of vitamin B6.
    GO:0070905    serine binding    Interacting selectively and non-covalently with 2-amino-3-hydroxypropanoic acid.
    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:0006565    L-serine catabolic process    The chemical reactions and pathways resulting in the breakdown of L-serine, the L-enantiomer of serine, i.e. (2S)-2-amino-3-hydroxypropanoic acid.
    GO:0006563    L-serine metabolic process    The chemical reactions and pathways involving L-serine, the L-enantiomer of serine, i.e. (2S)-2-amino-3-hydroxypropanoic acid.
    GO:0045329    carnitine biosynthetic process    The chemical reactions and pathways resulting in the formation of carnitine (hydroxy-trimethyl aminobutyric acid), a compound that participates in the transfer of acyl groups across the inner mitochondrial membrane.
    GO:1904482    cellular response to tetrahydrofolate    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a tetrahydrofolate stimulus.
    GO:0006231    dTMP biosynthetic process    The chemical reactions and pathways resulting in the formation of dTMP, deoxyribosylthymine monophosphate (2'-deoxyribosylthymine 5'-phosphate).
    GO:0046655    folic acid metabolic process    The chemical reactions and pathways involving folic acid, pteroylglutamic acid. Folic acid is widely distributed as a member of the vitamin B complex and is essential for the synthesis of purine and pyrimidines.
    GO:0006545    glycine biosynthetic process    The chemical reactions and pathways resulting in the formation of glycine, aminoethanoic acid.
    GO:0019264    glycine biosynthetic process from serine    The chemical reactions and pathways resulting in the formation of glycine from other compounds, including serine.
    GO:0006544    glycine metabolic process    The chemical reactions and pathways involving glycine, aminoethanoic acid.
    GO:0006730    one-carbon metabolic process    The chemical reactions and pathways involving the transfer of one-carbon units in various oxidation states.
    GO:0051289    protein homotetramerization    The formation of a protein homotetramer, a macromolecular structure consisting of four noncovalently associated identical subunits.
    GO:0051262    protein tetramerization    The formation of a protein tetramer, a macromolecular structure consisting of four noncovalently associated identical or nonidentical subunits.
    GO:0009113    purine nucleobase biosynthetic process    The chemical reactions and pathways resulting in the formation of purine nucleobases, one of the two classes of nitrogen-containing ring compounds found in DNA and RNA, which include adenine and guanine.
    GO:0035999    tetrahydrofolate interconversion    The chemical reactions and pathways by which one-carbon (C1) units are transferred between tetrahydrofolate molecules, to synthesise other tetrahydrofolate molecules.
    GO:0046653    tetrahydrofolate metabolic process    The chemical reactions and pathways involving tetrahydrofolate, 5,6,7,8-tetrahydrofolic acid, a folate derivative bearing additional hydrogens on the pterin group.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.


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