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(-) Description

Title :  E75L MUTANT OF RABBIT CYTOSOLIC SERINE HYDROXYMETHYLTRANSFERASE, COMPLEX WITH GLYCINE
 
Authors :  D. M. Szebenyi, F. N. Musayev, M. L. Di Salvo, M. K. Safo, V. Schirch
Date :  12 Dec 03  (Deposition) - 15 Jun 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  One-Carbon Metabolism, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  D. M. Szebenyi, F. N. Musayev, M. L. Di Salvo, M. K. Safo, V. Schirch
Serine Hydroxymethyltransferase: Role Of Glu75 And Evidence That Serine Is Cleaved By A Retroaldol Mechanism.
Biochemistry V. 43 6865 2004
PubMed-ID: 15170323  |  Reference-DOI: 10.1021/BI049791Y

(-) Compounds

Molecule 1 - SERINE HYDROXYMETHYLTRANSFERASE, CYTOSOLIC
    ChainsA, B
    EC Number2.1.2.1
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET22B
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneSHMT1
    MutationYES
    Organism CommonRABBIT
    Organism ScientificORYCTOLAGUS CUNICULUS
    Organism Taxid9986
    SynonymSERINE METHYLASE, GLYCINE HYDROXYMETHYLTRANSFERASE, SHMT

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric Unit (3, 5)
No.NameCountTypeFull Name
1GLY1Mod. Amino AcidGLYCINE
2PLP2Ligand/IonPYRIDOXAL-5'-PHOSPHATE
3PO42Ligand/IonPHOSPHATE ION
Biological Unit 1 (3, 10)
No.NameCountTypeFull Name
1GLY2Mod. Amino AcidGLYCINE
2PLP4Ligand/IonPYRIDOXAL-5'-PHOSPHATE
3PO44Ligand/IonPHOSPHATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:53 , HIS A:231 , ARG A:402 , PLP A:500 , TYR B:73 , TYR B:83BINDING SITE FOR RESIDUE PO4 A 501
2AC2SOFTWARETYR A:73 , TYR A:83 , SER B:53 , SER B:203 , HIS B:231 , LYS B:257 , ARG B:402 , PLP B:600BINDING SITE FOR RESIDUE PO4 B 601
3AC3SOFTWARETYR A:73 , LEU A:75 , TYR A:83 , SER B:53 , HIS B:231 , LYS B:257 , ARG B:402 , PLP B:600BINDING SITE FOR RESIDUE GLY B 602
4AC4SOFTWARESER A:119 , GLY A:120 , SER A:121 , HIS A:148 , SER A:203 , ASP A:228 , ALA A:230 , HIS A:231 , THR A:254 , HIS A:256 , LYS A:257 , PO4 A:501 , HOH A:515 , TYR B:73 , GLY B:303BINDING SITE FOR RESIDUE PLP A 500
5AC5SOFTWARETYR A:73 , TYR A:118 , GLY A:303 , SER B:119 , GLY B:120 , SER B:121 , HIS B:148 , THR B:202 , SER B:203 , ASP B:228 , ALA B:230 , HIS B:231 , THR B:254 , HIS B:256 , LYS B:257 , PO4 B:601 , GLY B:602BINDING SITE FOR RESIDUE PLP B 600

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1RV3)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Phe A:297 -Pro A:298
2Phe B:297 -Pro B:298

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1RV3)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SHMTPS00096 Serine hydroxymethyltransferase pyridoxal-phosphate attachment site.GLYC_RABIT249-265
 
  2A:249-265
B:249-265
Biological Unit 1 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SHMTPS00096 Serine hydroxymethyltransferase pyridoxal-phosphate attachment site.GLYC_RABIT249-265
 
  4A:249-265
B:249-265

(-) Exons   (0, 0)

(no "Exon" information available for 1RV3)

(-) 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:463
 aligned with GLYC_RABIT | P07511 from UniProtKB/Swiss-Prot  Length:484

    Alignment length:470
                                    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       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484
           GLYC_RABIT    15 WSSHEQMLAQPLKDSDAEVYDIIKKESNRQRVGLELIASENFASRAVLEALGSCLNNKYSEGYPGQRYYGGTEHIDELETLCQKRALQAYGLDPQCWGVNVQPYSGSPANFAVYTALVEPHGRIMGLDLPDGGHLTHGFMTDKKKISATSIFFESMAYKVNPDTGYIDYDRLEENARLFHPKLIIAGTSCYSRNLDYGRLRKIADENGAYLMADMAHISGLVVAGVVPSPFEHCHVVTTTTHKTLRGCRAGMIFYRRGVRSVDPKTGKEILYNLESLINSAVFPGLQGGPHNHAIAGVAVALKQAMTPEFKEYQRQVVANCRALSAALVELGYKIVTGGSDNHLILVDLRSKGTDGGRAEKVLEACSIACNKNTCPGDKSALRPSGLRLGTPALTSRGLLEKDFQKVAHFIHRGIELTVQIQDDTGPRATLKEFKEKLAGDEKHQRAVRALRQEVESFAALFPLPGLPGF 484
               SCOP domains d1rv3a_ A: Serine hydroxymethyltransferase                                                                                                                                                                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains ---------------1rv3A01 A:30-54,A:330-4741rv3A02 A:55-329 Type I PLP-dependent aspartate aminotransferase-like (Major domain)                                                                                                                                                                                               1rv3A01 A:30-54,A:330-474 Aspartate Aminotransferase, domain 1                                                                                   ---------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhh..hhhhhhhhhhhhhhhhhhhhhh.ee........hhhhhhhhhhhhhh....ee..ee....hhhhhhhhhhhhhhhhhhh......eeee....hhhhhhhhhhhhhh....eeeee.hhhh.hhhhh........hhhhhhheeeee.........hhhhhhhhhhhhh..eeee.........hhhhhhhhhhhh..eeeee...hhhhhhhh...hhhhh..eeeee.hhhhh....eeeeee.....-------....hhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..ee.hhh....eeeee.hhhh.hhhhhhhhhhhh.ee.eee............eeeeehhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------SHMT             --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1rv3 A  15 WSSHEQMLAQPLKDSDAEVYDIIKKESNRQRVGLELIASENFASRAVLEALGSCLNNKYSLGYPGQRYYGGTEHIDELETLCQKRALQAYGLDPQCWGVNVQPYSGSPANFAVYTALVEPHGRIMGLDLPDGGHLTHGFMTDKKKISATSIFFESMAYKVNPDTGYIDYDRLEENARLFHPKLIIAGTSCYSRNLDYGRLRKIADENGAYLMADMAHISGLVVAGVVPSPFEHCHVVTTTTHKTLRGCRAGMIFYRRGVRS-------EILYNLESLINSAVFPGLQGGPHNHAIAGVAVALKQAMTPEFKEYQRQVVANCRALSAALVELGYKIVTGGSDNHLILVDLRSKGTDGGRAEKVLEACSIACNKNTCPGDKSALRPSGLRLGTPALTSRGLLEKDFQKVAHFIHRGIELTVQIQDDTGPRATLKEFKEKLAGDEKHQRAVRALRQEVESFAALFPLPGLPGF 484
                                    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       274|      284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484
                                                                                                                                                                                                                                                                                              275     283                                                                                                                                                                                                         

Chain B from PDB  Type:PROTEIN  Length:466
 aligned with GLYC_RABIT | P07511 from UniProtKB/Swiss-Prot  Length:484

    Alignment length:470
                                    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       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484
           GLYC_RABIT    15 WSSHEQMLAQPLKDSDAEVYDIIKKESNRQRVGLELIASENFASRAVLEALGSCLNNKYSEGYPGQRYYGGTEHIDELETLCQKRALQAYGLDPQCWGVNVQPYSGSPANFAVYTALVEPHGRIMGLDLPDGGHLTHGFMTDKKKISATSIFFESMAYKVNPDTGYIDYDRLEENARLFHPKLIIAGTSCYSRNLDYGRLRKIADENGAYLMADMAHISGLVVAGVVPSPFEHCHVVTTTTHKTLRGCRAGMIFYRRGVRSVDPKTGKEILYNLESLINSAVFPGLQGGPHNHAIAGVAVALKQAMTPEFKEYQRQVVANCRALSAALVELGYKIVTGGSDNHLILVDLRSKGTDGGRAEKVLEACSIACNKNTCPGDKSALRPSGLRLGTPALTSRGLLEKDFQKVAHFIHRGIELTVQIQDDTGPRATLKEFKEKLAGDEKHQRAVRALRQEVESFAALFPLPGLPGF 484
               SCOP domains d1rv3b_ B: Serine hydroxymethyltransferase                                                                                                                                                                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains ---------------1rv3B01 B:30-54,B:330-4841rv3B02 B:55-329 Type I PLP-dependent aspartate aminotransferase-like (Major domain)                                                                                                                                                                                               1rv3B01 B:30-54,B:330-484 Aspartate Aminotransferase, domain 1                                                                                              CATH domains
           Pfam domains (1) -----------SHMT-1rv3B01 B:26-425                                                                                                                                                                                                                                                                                                                                                                                           ----------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) -----------SHMT-1rv3B02 B:26-425                                                                                                                                                                                                                                                                                                                                                                                           ----------------------------------------------------------- Pfam domains (2)
         Sec.struct. author hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh.ee........hhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhh......eeee....hhhhhhhhhhhhhh....eeeee.hhhh.hhhhh........hhhhhhheeeee.........hhhhhhhhhhhhh..eeee.........hhhhhhhhhhhh..eeeee...hhhhhhh....hhhhh..eeeee.hhhhh....eeeeee..eee..----..ee.hhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..ee.hhh....eeeee.hhhh.hhhhhhhhhhhh.ee.eee............eeeeehhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------SHMT             --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1rv3 B  15 WSSHEQMLAQPLKDSDAEVYDIIKKESNRQRVGLELIASENFASRAVLEALGSCLNNKYSLGYPGQRYYGGTEHIDELETLCQKRALQAYGLDPQCWGVNVQPYSGSPANFAVYTALVEPHGRIMGLDLPDGGHLTHGFMTDKKKISATSIFFESMAYKVNPDTGYIDYDRLEENARLFHPKLIIAGTSCYSRNLDYGRLRKIADENGAYLMADMAHISGLVVAGVVPSPFEHCHVVTTTTHKTLRGCRAGMIFYRRGVRSVD----KEILYNLESLINSAVFPGLQGGPHNHAIAGVAVALKQAMTPEFKEYQRQVVANCRALSAALVELGYKIVTGGSDNHLILVDLRSKGTDGGRAEKVLEACSIACNKNTCPGDKSALRPSGLRLGTPALTSRGLLEKDFQKVAHFIHRGIELTVQIQDDTGPRATLKEFKEKLAGDEKHQRAVRALRQEVESFAALFPLPGLPGF 484
                                    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       274  |    284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484
                                                                                                                                                                                                                                                                                                277  282                                                                                                                                                                                                          

   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

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit

(-) Gene Ontology  (23, 23)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (GLYC_RABIT | P07511)
molecular function
    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: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: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: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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 Related Entries

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

UniProtKB/Swiss-Prot
        GLYC_RABIT | P075111cj0 1ls3 1rv4 1rvu 1rvy

(-) Related Entries Specified in the PDB File

1cj0 WILD-TYPE RABBIT CSHMT.
1ls3 WILD-TYPE RABBIT CSHMT IN COMPLEX WITH GLYCINE AND 5- FORMYLTETRAHYDROPTEROYLTRIGLUTAMATE.