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(-) Description

Title :  REFINEMENT AND COMPARISON OF THE CRYSTAL STRUCTURES OF PIG CYTOSOLIC ASPARTATE AMINOTRANSFERASE AND ITS COMPLEX WITH 2-METHYLASPARTATE
 
Authors :  S. Rhee, M. M. Silva, C. C. Hyde, P. H. Rogers, C. M. Metzler, D. E. Metzler, A. Arnone
Date :  08 May 97  (Deposition) - 20 Aug 97  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Cytosolic Aspartate Aminotransferase, Pig, In The Presence Of Ligand 2-Methylaspartate, Aminotransferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. Rhee, M. M. Silva, C. C. Hyde, P. H. Rogers, C. M. Metzler, D. E. Metzler, A. Arnone
Refinement And Comparisons Of The Crystal Structures Of Pig Cytosolic Aspartate Aminotransferase And Its Complex With 2-Methylaspartate.
J. Biol. Chem. V. 272 17293 1997
PubMed-ID: 9211866  |  Reference-DOI: 10.1074/JBC.272.28.17293
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ASPARTATE AMINOTRANSFERASE
    ChainsA
    EC Number2.6.1.1
    Organism CommonPIG
    Organism ScientificSUS SCROFA
    Organism Taxid9823
    Other DetailsTHE COENZYME PYRIDOXAL 5'-PHOSPHATE IN SUBUNIT A FORMS A SCHIFF BASE WITH THE SUBSTRATE ANALOG 2- METHYLASPARTATE, AND FORMS THE EXTERNAL ALDIMINE. BUT DUE TO CRYSTAL LATTICE PACKINGS THE COENZYME IN SUBUNIT B IS STILL IN THE INTERNAL ALDIMINE WITH THE SIDE CHAIN OF LYS 258.
 
Molecule 2 - ASPARTATE AMINOTRANSFERASE
    ChainsB
    EC Number2.6.1.1
    Organism CommonPIG
    Organism ScientificSUS SCROFA
    Organism Taxid9823
    Other DetailsTHE COENZYME PYRIDOXAL 5'-PHOSPHATE IN SUBUNIT A FORMS A SCHIFF BASE WITH THE SUBSTRATE ANALOG 2- METHYLASPARTATE, AND FORMS THE EXTERNAL ALDIMINE. BUT DUE TO CRYSTAL LATTICE PACKINGS THE COENZYME IN SUBUNIT B IS STILL IN THE INTERNAL ALDIMINE WITH THE SIDE CHAIN OF LYS 258.

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1LLP1Mod. Amino Acid2-LYSINE(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHANE)
2PLA1Ligand/Ion2-[(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL)-AMINO]-2-METHYL-SUCCINIC ACID

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL A:37 , GLY A:38 , GLY A:107 , GLY A:108 , THR A:109 , TRP A:140 , ASN A:194 , ASP A:222 , TYR A:225 , SER A:255 , SER A:257 , LYS A:258 , ARG A:266 , ARG A:386 , HOH A:562 , TYR B:70 , ARG B:292 , HOH B:554BINDING SITE FOR RESIDUE PLA A 415
2ACTUNKNOWNLLP B:258COENZYME BINDING SITES.
3AXTUNKNOWNPLA A:415SUBSTRATE BINDING SITES.

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Ser A:137 -Pro A:138
2Asn A:194 -Pro A:195
3Ser B:137 -Pro B:138
4Asn B:194 -Pro B:195

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1AA_TRANSFER_CLASS_1PS00105 Aminotransferases class-I pyridoxal-phosphate attachment site.AATC_PIG256-269
 
  2A:255-268
B:255-268

(-) Exons   (0, 0)

(no "Exon" information available for 1AJS)

(-) 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:412
 aligned with AATC_PIG | P00503 from UniProtKB/Swiss-Prot  Length:413

    Alignment length:412
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411  
             AATC_PIG     2 APPSVFAEVPQAQPVLVFKLIADFREDPDPRKVNLGVGAYRTDDCQPWVLPVVRKVEQRIANDSSLNHEYLPILGLAEFRTCASRLALGDDSPALQEKRVGGVQSLGGTGALRIGAEFLARWYNGTNNKDTPVYVSSPTWENHNGVFTTAGFKDIRSYRYWDTEKRGLDLQGFLSDLENAPEFSIFVLHACAHNPTGTDPTPEQWKQIASVMKRRFLFPFFDSAYQGFASGNLEKDAWAIRYFVSEGFELFCAQSFSKNFGLYNERVGNLTVVAKEPDSILRVLSQMEKIVRVTWSNPPAQGARIVARTLSDPELFHEWTGNVKTMADRILSMRSELRARLEALKTPGTWNHITDQIGMFSFTGLNPKQVEYLINEKHIYLLPSGRINMCGLTTKNLDYVATSIHEAVTKIQ 413
               SCOP domains d1ajsa_ A: Aspartate aminotransferase, AAT                                                                                                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains --------------1ajsA01 A:15-48,A:328-408         1ajsA02 A:49-327 Type I PLP-dependent aspartate aminotransferase-like (Major domain)                                                                                                                                                                                                   1ajsA01 A:15-48,A:328-408 Aspartate Aminotransferase, domain 1                   ---- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............hhhhhhhhhh.........................hhhhhhhhhhh...............hhhhhhhhhhhh....hhhh...eeeeeeehhhhhhhhhhhhhhhh..........eeeee...hhhhhhhhhh....eeeee..........hhhhhhhhhh.....eeeee............hhhhhhhhhhhhh...eeeeee.........hhhhhhhhhhhhh....eeeeee.......hhh.eeeeeee...hhhhhhhhhhhhhhhh........hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhh....eee....hhhhhhhhh..........eeehhh.....hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AA_TRANSFER_CL------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ajs A   1 APPSVFAEVPQAQPVLVFKLIADFREDPDPRKVNLGVGAYRTDDCQPWVLPVVRKVEQRIANNSSLNHEYLPILGLAEFRTCASRLALGDDSPALQEKRVGGVQSLGGTGALRIGAEFLARWYNGTNNKDTPVYVSSPTWENHNGVFTTAGFKDIRSYRYWDTEKRGLDLQGFLSDLENAPEFSIFVLHACAHNPTGTDPTPEQWKQIASVMKRRFLFPFFDSAYQGFASGNLEKDAWAIRYFVSEGFELFCAQSFSKNFGLYNERVGNLTVVAKEPDSILRVLSQMQKIVRVTWSNPPAQGARIVARTLSDPELFHEWTGNVKTMADRILSMRSELRARLEALKTPGTWNHITDQIGMFSFTGLNPKQVEYLINQKHIYLLPSGRINMCGLTTKNLDYVATSIHEAVTKIQ 412
                                    10        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  

Chain B from PDB  Type:PROTEIN  Length:412
 aligned with AATC_PIG | P00503 from UniProtKB/Swiss-Prot  Length:413

    Alignment length:412
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411  
             AATC_PIG     2 APPSVFAEVPQAQPVLVFKLIADFREDPDPRKVNLGVGAYRTDDCQPWVLPVVRKVEQRIANDSSLNHEYLPILGLAEFRTCASRLALGDDSPALQEKRVGGVQSLGGTGALRIGAEFLARWYNGTNNKDTPVYVSSPTWENHNGVFTTAGFKDIRSYRYWDTEKRGLDLQGFLSDLENAPEFSIFVLHACAHNPTGTDPTPEQWKQIASVMKRRFLFPFFDSAYQGFASGNLEKDAWAIRYFVSEGFELFCAQSFSKNFGLYNERVGNLTVVAKEPDSILRVLSQMEKIVRVTWSNPPAQGARIVARTLSDPELFHEWTGNVKTMADRILSMRSELRARLEALKTPGTWNHITDQIGMFSFTGLNPKQVEYLINEKHIYLLPSGRINMCGLTTKNLDYVATSIHEAVTKIQ 413
               SCOP domains d1ajsb_ B: Aspartate aminotransferase, AAT                                                                                                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains --------------1ajsB01 B:15-48,B:328-408         1ajsB02 B:49-327 Type I PLP-dependent aspartate aminotransferase-like (Major domain)                                                                                                                                                                                                   1ajsB01 B:15-48,B:328-408 Aspartate Aminotransferase, domain 1                   ---- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............hhhhhhhhhhh........................hhhhhhhhhhh...............hhhhhhhhhhhh....hhhh...eeeeeeehhhhhhhhhhhhhhhh..........eeee.....hhhhhhhh.....eeee...........hhhhhhhhh......eeeee............hhhhhhhhhhhhhh..eeeeee.........hhhhhhhhhhhhh....eeeeee.......hhh.eeeeeee...hhhhhhhhhhhhhhhh........hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhh....eee....hhhhhhhhhhh........eeehhh.....hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AA_TRANSFER_CL------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ajs B   1 APPSVFAEVPQAQPVLVFKLIADFREDPDPRKVNLGVGAYRTDDCQPWVLPVVRKVEQRIANNSSLNHEYLPILGLAEFRTCASRLALGDDSPALQEKRVGGVQSLGGTGALRIGAEFLARWYNGTNNKDTPVYVSSPTWENHNGVFTTAGFKDIRSYRYWDTEKRGLDLQGFLSDLENAPEFSIFVLHACAHNPTGTDPTPEQWKQIASVMKRRFLFPFFDSAYQGFASGNLEKDAWAIRYFVSEGFELFCAQSFSkNFGLYNERVGNLTVVAKEPDSILRVLSQMQKIVRVTWSNPPAQGARIVARTLSDPELFHEWTGNVKTMADRILSMRSELRARLEALKTPGTWNHITDQIGMFSFTGLNPKQVEYLINQKHIYLLPSGRINMCGLTTKNLDYVATSIHEAVTKIQ 412
                                    10        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  
                                                                                                                                                                                                                                                                                           258-LLP                                                                                                                                                      

   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  (0, 0)

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

(-) Gene Ontology  (30, 30)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (AATC_PIG | P00503)
molecular function
    GO:0004069    L-aspartate:2-oxoglutarate aminotransferase activity    Catalysis of the reaction: L-aspartate + 2-oxoglutarate = oxaloacetate + L-glutamate.
    GO:0047801    L-cysteine:2-oxoglutarate aminotransferase activity    Catalysis of the reaction: L-cysteine + 2-oxoglutarate = mercaptopyruvate + L-glutamate.
    GO:0080130    L-phenylalanine:2-oxoglutarate aminotransferase activity    Catalysis of the reaction: L-phenylalanine + 2-oxoglutarate = phenylpyruvate + L-glutamate.
    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:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0004609    phosphatidylserine decarboxylase activity    Catalysis of the reaction: H(+) + phosphatidyl-L-serine = CO(2) + phosphatidylethanolamine.
    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: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:0006103    2-oxoglutarate metabolic process    The chemical reactions and pathways involving oxoglutarate, the dianion of 2-oxoglutaric acid. It is a key constituent of the TCA cycle and a key intermediate in amino-acid metabolism.
    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:0006532    aspartate biosynthetic process    The chemical reactions and pathways resulting in the formation of aspartate, the anion derived from aspartic acid, 2-aminobutanedioic acid.
    GO:0006533    aspartate catabolic process    The chemical reactions and pathways resulting in the breakdown of aspartate, the anion derived from aspartic acid, 2-aminobutanedioic acid.
    GO:0006531    aspartate metabolic process    The chemical reactions and pathways involving aspartate, the anion derived from aspartic acid, 2-aminobutanedioic acid.
    GO:0009058    biosynthetic process    The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.
    GO:0008652    cellular amino acid biosynthetic process    The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents.
    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:0032869    cellular response to insulin stimulus    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 an insulin stimulus. Insulin is a polypeptide hormone produced by the islets of Langerhans of the pancreas in mammals, and by the homologous organs of other organisms.
    GO:0055089    fatty acid homeostasis    Any process involved in the maintenance of an internal steady state of fatty acid within an organism or cell.
    GO:0019551    glutamate catabolic process to 2-oxoglutarate    The chemical reactions and pathways resulting in the breakdown of glutamate into other compounds, including 2-oxoglutarate.
    GO:0019550    glutamate catabolic process to aspartate    The chemical reactions and pathways resulting in the breakdown of glutamate into other compounds, including aspartate.
    GO:0006536    glutamate metabolic process    The chemical reactions and pathways involving glutamate, the anion of 2-aminopentanedioic acid.
    GO:0006114    glycerol biosynthetic process    The chemical reactions and pathways resulting in the formation of glycerol, 1,2,3-propanetriol, a sweet, hygroscopic, viscous liquid, widely distributed in nature as a constituent of many lipids.
    GO:0006107    oxaloacetate metabolic process    The chemical reactions and pathways involving oxaloacetate, the anion of oxobutanedioic acid, an important intermediate in metabolism, especially as a component of the TCA cycle.
    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: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
        AATC_PIG | P005031ajr 5ton 5toq 5tor 5tot

(-) Related Entries Specified in the PDB File

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