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(-) Description

Title :  X-RAY CRYSTAL STRUCTURE OF HUMAN SERINE RACEMASE IN COMPLEX WITH MALONATE A POTENT INHIBITOR
 
Authors :  M. A. Smith, J. Barker, V. Mack, A. Ebneth, I. Moraes, B. Felicetti, A. Ce
Date :  23 Dec 09  (Deposition) - 26 Jan 10  (Release) - 12 May 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Pyridoxal Phosphate, Plp, Serine Racemase, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. A. Smith, V. Mack, A. Ebneth, I. Moraes, B. Felicetti, M. Wood, D. Schonfeld, O. Mather, A. Cesura, J. Barker
The Structure Of Mammalian Serine Racemase: Evidence For Conformational Changes Upon Inhibitor Binding.
J. Biol. Chem. V. 285 12873 2010
PubMed-ID: 20106978  |  Reference-DOI: 10.1074/JBC.M109.050062

(-) Compounds

Molecule 1 - SERINE RACEMASE
    ChainsA
    EC Number5.1.1.18
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET24A
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneSRR
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (2x)A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (3, 3)
No.NameCountTypeFull Name
1MLI1Ligand/IonMALONATE ION
2MN1Ligand/IonMANGANESE (II) ION
3PLP1Ligand/IonPYRIDOXAL-5'-PHOSPHATE
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1MLI2Ligand/IonMALONATE ION
2MN-1Ligand/IonMANGANESE (II) ION
3PLP2Ligand/IonPYRIDOXAL-5'-PHOSPHATE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:55 , LYS A:56 , ASN A:86 , GLY A:185 , GLY A:186 , GLY A:187 , GLY A:188 , MET A:189 , VAL A:240 , GLU A:283 , THR A:285 , SER A:313 , GLY A:314 , MLI A:348 , HOH A:355 , HOH A:375 , HOH A:403 , HOH A:436BINDING SITE FOR RESIDUE PLP A 350
2AC2SOFTWAREGLU A:210 , ALA A:214 , ASP A:216 , HOH A:360 , HOH A:376 , HOH A:392BINDING SITE FOR RESIDUE MN A 347
3AC3SOFTWARELYS A:56 , SER A:83 , SER A:84 , ASN A:86 , HIS A:87 , ARG A:135 , GLY A:239 , SER A:242 , PLP A:350 , HOH A:351 , HOH A:373 , HOH A:403BINDING SITE FOR RESIDUE MLI A 348

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3L6B)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3L6B)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3L6B)

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DEHYDRATASE_SER_THRPS00165 Serine/threonine dehydratases pyridoxal-phosphate attachment site.SRR_HUMAN47-60  1A:47-60
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DEHYDRATASE_SER_THRPS00165 Serine/threonine dehydratases pyridoxal-phosphate attachment site.SRR_HUMAN47-60  2A:47-60

(-) Exons   (0, 0)

(no "Exon" information available for 3L6B)

(-) 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:322
 aligned with SRR_HUMAN | Q9GZT4 from UniProtKB/Swiss-Prot  Length:340

    Alignment length:327
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       
            SRR_HUMAN     3 AQYCISFADVEKAHINIRDSIHLTPVLTSSILNQLTGRNLFFKCELFQKTGSFKIRGALNAVRSLVPDALERKPKAVVTHSSGNHGQALTYAAKLEGIPAYIVVPQTAPDCKKLAIQAYGASIVYCEPSDESRENVAKRVTEETEGIMVHPNQEPAVIAGQGTIALEVLNQVPLVDALVVPVGGGGMLAGIAITVKALKPSVKVYAAEPSNADDCYQSKLKGKLMPNLYPPETIADGVKSSIGLNTWPIIRDLVDDIFTVTEDEIKCATQLVWERMKLLIEPTAGVGVAAVLSQHFQTVSPEVKNICIVLSGGNVDLTSSITWVKQA 329
               SCOP domains d3l6ba_ A: automated matches                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------PALP-3l6bA01 A:19-314                                                                                                                                                                                                                                                                                   --------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhh....ee.hhhhhhhhh.eeeeee.hhhhhhhhhhhhhhhhhhh..-----.....eeee..hhhhhhhhhhhhhh...eeeeee...hhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhhhh.ee.....hhhhhhhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhhhhh...eeeeeee...hhhhhhhhhh............hhhhh.....hhhhhhhhhh.eeeeehhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh.....eeeeee.......hhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------DEHYDRATASE_SE----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3l6b A   3 AQYDISFADVEKAHINIRDSIHLTPVLTSSILNQLTGRNLFFKCELFQKTGSFKIRGALNAVRSLV-----RKPKAVVTHSSGNHGQALTYAAKLEGIPAYIVVPQTAPDCKKLAIQAYGASIVYCEPSDESRENVAKRVTEETEGIMVHPNQEPAVIAGQGTIALEVLNQVPLVDALVVPVGGGGMLAGIAITVKALKPSVKVYAAEPSNADDCYQSKLKGKLMPNLYPPETIADGVKSSIGLNTWPIIRDLVDDIFTVTEDEIKCATQLVWERMKLLIEPTAGVGVAAVLSQHFQTVSPEVKNICIVLSGGNVDLTSSITWVKQA 329
                                    12        22        32        42        52        62     |   - |      82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       
                                                                                            68    74                                                                                                                                                                                                                                                               

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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 Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3L6B)

(-) Pfam Domains  (1, 1)

Asymmetric Unit

(-) Gene Ontology  (34, 34)

Asymmetric Unit(hide GO term definitions)
Chain A   (SRR_HUMAN | Q9GZT4)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0008721    D-serine ammonia-lyase activity    Catalysis of the reaction: D-serine = pyruvate + NH3.
    GO:0003941    L-serine ammonia-lyase activity    Catalysis of the reaction: L-serine = pyruvate + NH3.
    GO:0030165    PDZ domain binding    Interacting selectively and non-covalently with a PDZ domain of a protein, a domain found in diverse signaling proteins.
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    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:0016594    glycine binding    Interacting selectively and non-covalently with glycine, aminoethanoic acid.
    GO:0016853    isomerase activity    Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
    GO:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
    GO:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    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:0030378    serine racemase activity    Catalysis of the synthesis of free D-serine from L-serine.
    GO:0018114    threonine racemase activity    Catalysis of the reaction: L-threonine = D-threonine.
biological process
    GO:0070179    D-serine biosynthetic process    The chemical reactions and pathways resulting in the formation of D-serine, the D-enantiomer of serine, i.e. (2R)-2-amino-3-hydroxypropanoic acid. D-serine is often formed by racemization of L-serine.
    GO:0070178    D-serine metabolic process    The chemical reactions and pathways involving D-serine, the D-enantiomer of serine, i.e. (2R)-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:0007568    aging    A developmental process that is a deterioration and loss of function over time. Aging includes loss of functions such as resistance to disease, homeostasis, and fertility, as well as wear and tear. Aging includes cellular senescence, but is more inclusive. May precede death and may succeed developmental maturation (GO:0021700).
    GO:0007420    brain development    The process whose specific outcome is the progression of the brain over time, from its formation to the mature structure. Brain development begins with patterning events in the neural tube and ends with the mature structure that is the center of thought and emotion. The brain is responsible for the coordination and control of bodily activities and the interpretation of information from the senses (sight, hearing, smell, etc.).
    GO:0006520    cellular amino acid metabolic process    The chemical reactions and pathways involving amino acids, carboxylic acids containing one or more amino groups, as carried out by individual cells.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    GO:0051289    protein homotetramerization    The formation of a protein homotetramer, a macromolecular structure consisting of four noncovalently associated identical subunits.
    GO:0042866    pyruvate biosynthetic process    The chemical reactions and pathways resulting in the formation of pyruvate, 2-oxopropanoate.
    GO:0042493    response to drug    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease.
    GO:0032496    response to lipopolysaccharide    Any process that results in a change in state or activity of an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a lipopolysaccharide stimulus; lipopolysaccharide is a major component of the cell wall of gram-negative bacteria.
    GO:0043278    response to morphine    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a morphine stimulus. Morphine is an opioid alkaloid, isolated from opium, with a complex ring structure.
    GO:0014070    response to organic cyclic compound    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an organic cyclic compound stimulus.
    GO:0009069    serine family amino acid metabolic process    The chemical reactions and pathways involving amino acids of the serine family, comprising cysteine, glycine, homoserine, selenocysteine and serine.
cellular component
    GO:0045177    apical part of cell    The region of a polarized cell that forms a tip or is distal to a base. For example, in a polarized epithelial cell, the apical region has an exposed surface and lies opposite to the basal lamina that separates the epithelium from other tissue.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0043025    neuronal cell body    The portion of a neuron that includes the nucleus, but excludes cell projections such as axons and dendrites.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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 Related Entries

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

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        SRR_HUMAN | Q9GZT43l6r

(-) Related Entries Specified in the PDB File

3l6c 3l6r