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(-) Description

Title :  CRYSTAL STRUCTURE OF PUTATIVE AMINOTRANSFERASE (AAH25799.1) FROM MUS MUSCULUS AT 1.80 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  29 Oct 09  (Deposition) - 10 Nov 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Putative Aminotransferase, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Putative Aminotransferase (Aah25799. 1) From Mus Musculus At 1. 80 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - ALANINE-GLYOXYLATE AMINOTRANSFERASE
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPRSPEEDET
    Expression System StrainHEK293
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneAAH25799.1, AGXT, MCG_16569
    Organism CommonMOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    SynonymALANINE-GLYOXYLATE AMINOTRANSFERASE ISOFORM CRA_B

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 12)

Asymmetric/Biological Unit (3, 12)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2EDO9Ligand/Ion1,2-ETHANEDIOL
3MG1Ligand/IonMAGNESIUM ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:54 , LEU A:55 , HOH A:789 , MET B:67BINDING SITE FOR RESIDUE CL A 502
02AC2SOFTWAREHIS A:319 , HIS A:323 , ASP A:396 , HOH A:678 , HOH A:679BINDING SITE FOR RESIDUE MG A 503
03AC3SOFTWAREGLU A:315 , THR A:392 , HOH A:700 , HOH A:744 , ARG B:403 , HOH B:740BINDING SITE FOR RESIDUE EDO A 504
04AC4SOFTWAREPHE A:113 , LEU A:116 , GLU A:117 , PRO A:118 , ILE A:141 , ARG A:255 , PRO A:259 , VAL A:260BINDING SITE FOR RESIDUE EDO A 505
05AC5SOFTWAREARG A:93 , PRO A:95 , VAL A:145 , ASP A:246 , HOH A:603 , HOH A:626 , HOH A:813BINDING SITE FOR RESIDUE EDO A 507
06AC6SOFTWAREPRO A:187 , LEU A:188 , ASP A:189 , HOH A:628 , HOH A:801 , HOH A:820BINDING SITE FOR RESIDUE EDO A 508
07AC7SOFTWAREGLU A:109 , GLU B:109 , HOH B:665BINDING SITE FOR RESIDUE EDO A 510
08AC8SOFTWAREGLY A:190 , HOH A:672 , HOH A:681 , ARG B:255BINDING SITE FOR RESIDUE EDO A 511
09AC9SOFTWAREARG A:66 , MET A:67 , ASN B:54 , LEU B:55 , HOH B:768BINDING SITE FOR RESIDUE CL B 501
10BC1SOFTWAREPHE B:113 , LEU B:116 , GLU B:117 , ILE B:141 , ARG B:255 , PRO B:259 , VAL B:260BINDING SITE FOR RESIDUE EDO B 506
11BC2SOFTWAREILE B:129 , ARG B:133 , HOH B:671BINDING SITE FOR RESIDUE EDO B 509
12BC3SOFTWARELEU B:188 , ASP B:189 , HOH B:620 , HOH B:758 , HOH B:814BINDING SITE FOR RESIDUE EDO B 512

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Gly A:51 -Pro A:52
2Gly B:51 -Pro B:52
3Pro B:236 -Pro B:237

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1AA_TRANSFER_CLASS_5PS00595 Aminotransferases class-V pyridoxal-phosphate attachment site.SPYA_MOUSE222-242
 
  2A:222-242
B:222-242

(-) Exons   (0, 0)

(no "Exon" information available for 3KGX)

(-) 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:383
 aligned with SPYA_MOUSE | O35423 from UniProtKB/Swiss-Prot  Length:414

    Alignment length:386
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406      
           SPYA_MOUSE    27 QLLVPPPEALSKPLSVPTRLLLGPGPSNLAPRVLAAGSLRMIGHMQKEMLQIMEEIKQGIQYVFQTRNPLTLVVSGSGHCAMETALFNLLEPGDSFLTGTNGIWGMRAAEIADRIGARVHQMIKKPGEHYTLQEVEEGLAQHKPVLLFLVHGESSTGVVQPLDGFGELCHRYQCLLLVDSVASLGGVPIYMDQQGIDIMYSSSQKVLNAPPGISLISFNDKAKYKVYSRKTKPVSFYTDITYLAKLWGCEGETRVIHHTTPVTSLYCLRESLALIAEQGLENCWRRHREATAHLHKHLQEMGLKFFVKDPEIRLPTITTVTVPAGYNWRDIVSYVLDHFSIEISGGLGPTEERVLRIGLLGYNATTENVDRVAEALREALQHCPKN 412
               SCOP domains d3kgxa_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains 3kgxA01 A:27-55,A:305-412    3kgxA02 A:56-304 Type I PLP-dependent aspartate aminotransferase-like (Major domain)                                                                                                                                                                     3kgxA01 A:27-55,A:305-412 Aspartate Aminotransferase, domain 1                                               CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhh.......ee........hhhhhhhh........hhhhhhhhhhhhhhhhhhhh....eeeeee....hhhhhhhhhhh....eeeeee.hhhhhhhhhhhhhh..eeeeee.......hhhhhhhhhhhhh..eeeee.ee....ee....hhhhhhhhh..eeeee..................eeeee..........eeeeeehhhhhhhhhh..........hhhhhhhhh....---......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhh...eeeee.....hhhhhhhhhhhhhhee....hhhhh..eeeee.hhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AA_TRANSFER_CLASS_5  -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kgx A  27 QLLVPPPEALSKPLSVPTRLLLGPGPSNLAPRVLAAGSLRMIGHMQKEMLQIMEEIKQGIQYVFQTRNPLTLVVSGSGHCAMETALFNLLEPGDSFLTGTNGIWGMRAAEIADRIGARVHQMIKKPGEHYTLQEVEEGLAQHKPVLLFLVHGESSTGVVQPLDGFGELCHRYQCLLLVDSVASLGGVPIYMDQQGIDIMYSSSQKVLNAPPGISLISFNDKAKYKVYSRKTKPVSFYTDITYLAKLWGCEG---VIHHTTPVTSLYCLRESLALIAEQGLENCWRRHREATAHLHKHLQEMGLKFFVKDPEIRLPTITTVTVPAGYNWRDIVSYVLDHFSIEISGGLGPTEERVLRIGLLGYNATTENVDRVAEALREALQHCPKN 412
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276|   |  286       296       306       316       326       336       346       356       366       376       386       396       406      
                                                                                                                                                                                                                                                                                    277 281                                                                                                                                   

Chain B from PDB  Type:PROTEIN  Length:390
 aligned with SPYA_MOUSE | O35423 from UniProtKB/Swiss-Prot  Length:414

    Alignment length:390
                                    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       332       342       352       362       372       382       392       402       412
           SPYA_MOUSE    23 MGSYQLLVPPPEALSKPLSVPTRLLLGPGPSNLAPRVLAAGSLRMIGHMQKEMLQIMEEIKQGIQYVFQTRNPLTLVVSGSGHCAMETALFNLLEPGDSFLTGTNGIWGMRAAEIADRIGARVHQMIKKPGEHYTLQEVEEGLAQHKPVLLFLVHGESSTGVVQPLDGFGELCHRYQCLLLVDSVASLGGVPIYMDQQGIDIMYSSSQKVLNAPPGISLISFNDKAKYKVYSRKTKPVSFYTDITYLAKLWGCEGETRVIHHTTPVTSLYCLRESLALIAEQGLENCWRRHREATAHLHKHLQEMGLKFFVKDPEIRLPTITTVTVPAGYNWRDIVSYVLDHFSIEISGGLGPTEERVLRIGLLGYNATTENVDRVAEALREALQHCPKN 412
               SCOP domains d3kgxb_ B: automated matches                                                                                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains 3kgxB01 B:23-55,B:305-412        3kgxB02 B:56-304 Type I PLP-dependent aspartate aminotransferase-like (Major domain)                                                                                                                                                                     3kgxB01 B:23-55,B:305-412 Aspartate Aminotransferase, domain 1                                               CATH domains
           Pfam domains (1) -----------------------Aminotran_5-3kgxB01 B:46-397                                                                                                                                                                                                                                                                                                                                    --------------- Pfam domains (1)
           Pfam domains (2) -----------------------Aminotran_5-3kgxB02 B:46-397                                                                                                                                                                                                                                                                                                                                    --------------- Pfam domains (2)
         Sec.struct. author ..........hhhhhh.......ee........hhhhhhhh........hhhhhhhhhhhhhhhhhhhh....eeeeee....hhhhhhhhhhh....eeeeee.hhhhhhhhhhhhhh..eeeeee.......hhhhhhhhhhhhh..eeeee.ee....ee....hhhhhhhhh..eeeee..................eeeee..........eeeeeehhhhhhhhhh..........hhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhh...eeeee.....hhhhhhhhhhhhhhee....hhhhh..eeeee.hhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AA_TRANSFER_CLASS_5  -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3kgx B  23 MGSYQLLVPPPEALSKPLSVPTRLLLGPGPSNLAPRVLAAGSLRMIGHMQKEMLQIMEEIKQGIQYVFQTRNPLTLVVSGSGHCAMETALFNLLEPGDSFLTGTNGIWGMRAAEIADRIGARVHQMIKKPGEHYTLQEVEEGLAQHKPVLLFLVHGESSTGVVQPLDGFGELCHRYQCLLLVDSVASLGGVPIYMDQQGIDIMYSSSQKVLNAPPGISLISFNDKAKYKVYSRKTKPVSFYTDITYLAKLWGCEGETRVIHHTTPVTSLYCLRESLALIAEQGLENCWRRHREATAHLHKHLQEMGLKFFVKDPEIRLPTITTVTVPAGYNWRDIVSYVLDHFSIEISGGLGPTEERVLRIGLLGYNATTENVDRVAEALREALQHCPKN 412
                                    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       332       342       352       362       372       382       392       402       412

   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/Biological Unit

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit

(-) Gene Ontology  (25, 25)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (SPYA_MOUSE | O35423)
molecular function
    GO:0008453    alanine-glyoxylate transaminase activity    Catalysis of the reaction: L-alanine + glyoxylate = pyruvate + glycine.
    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:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
    GO:0043621    protein self-association    Interacting selectively and non-covalently with a domain within the same polypeptide.
    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:0005102    receptor binding    Interacting selectively and non-covalently with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.
    GO:0004760    serine-pyruvate transaminase activity    Catalysis of the reaction: L-serine + pyruvate = 3-hydroxypyruvate + L-alanine.
    GO:0008483    transaminase activity    Catalysis of the transfer of an amino group to an acceptor, usually a 2-oxo 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:0042853    L-alanine catabolic process    The chemical reactions and pathways resulting in the breakdown of L-alanine, the L-enantiomer of 2-aminopropanoic acid, i.e. (2S)-2-aminopropanoic acid.
    GO:0019448    L-cysteine catabolic process    The chemical reactions and pathways resulting in the breakdown of L-cysteine, the L-enantiomer of 2-amino-3-mercaptopropanoic acid, i.e. (2R)-2-amino-3-mercaptopropanoic acid.
    GO:0007219    Notch signaling pathway    A series of molecular signals initiated by the binding of an extracellular ligand to the receptor Notch on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription.
    GO:0019265    glycine biosynthetic process, by transamination of glyoxylate    The chemical reactions and pathways resulting in the formation of glycine by the transamination of glyoxylate.
    GO:0009436    glyoxylate catabolic process    The chemical reactions and pathways resulting in the breakdown of glyoxylate, the anion of glyoxylic acid, HOC-COOH.
    GO:0046487    glyoxylate metabolic process    The chemical reactions and pathways involving glyoxylate, the anion of glyoxylic acid, HOC-COOH.
    GO:0046724    oxalic acid secretion    The controlled release of oxalic acid, ethanedioic acid, by a cell or a tissue.
    GO:0010498    proteasomal protein catabolic process    The chemical reactions and pathways resulting in the breakdown of a protein or peptide by hydrolysis of its peptide bonds that is mediated by the proteasome.
    GO:0042866    pyruvate biosynthetic process    The chemical reactions and pathways resulting in the formation of pyruvate, 2-oxopropanoate.
    GO:0051591    response to cAMP    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 cAMP (cyclic AMP, adenosine 3',5'-cyclophosphate) stimulus.
    GO:0051384    response to glucocorticoid    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 glucocorticoid stimulus. Glucocorticoids are hormonal C21 corticosteroids synthesized from cholesterol with the ability to bind with the cortisol receptor and trigger similar effects. Glucocorticoids act primarily on carbohydrate and protein metabolism, and have anti-inflammatory effects.
cellular component
    GO:0005759    mitochondrial matrix    The gel-like material, with considerable fine structure, that lies in the matrix space, or lumen, of a mitochondrion. It contains the enzymes of the tricarboxylic acid cycle and, in some organisms, the enzymes concerned with fatty acid oxidation.
    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:0005782    peroxisomal matrix    The volume contained within the membranes of a peroxisome; in many cells the matrix contains a crystalloid core largely composed of urate oxidase.
    GO:0005777    peroxisome    A small organelle enclosed by a single membrane, and found in most eukaryotic cells. Contains peroxidases and other enzymes involved in a variety of metabolic processes including free radical detoxification, lipid catabolism and biosynthesis, and hydrogen peroxide metabolism.

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 Related Entries

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

UniProtKB/Swiss-Prot
        SPYA_MOUSE | O354233kgw

(-) Related Entries Specified in the PDB File

3kgw THE SAME PROTEIN WITH PARTIALLY OCCUPIED ENDOGENOUS PYRIDOXAL-5'-PHOSPHATE BOUND