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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN PEROXISOMAL ACETYL-COA ACYL TRANSFERASE 1 (ACAA1)
 
Authors :  E. Papagrigoriou, C. Johansson, C. Smee, K. Kavanagh, A. C. W. Pike, M. S J. Weigelt, A. Edwards, C. H. Arrowsmith, O. Gileadi, F. Gorrec, C. Ume Delft, U. Oppermann, Structural Genomics Consortium (Sgc)
Date :  28 Sep 06  (Deposition) - 10 Oct 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.55
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Fatty Acid Metabolism, Structural Genomics, Structural Genomics Consortium, Sgc, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  E. Papagrigoriou, C. Johansson, C. Smee, K. Kavanagh, A. C. W. Pike, M. Sundstrom, J. Weigelt, A. Edwards, C. H. Arrowsmith, O. Gileadi, F. Gorrec, C. Umeano, F. Von Delft, U. Oppermann, Structural Genomics Consortium (Sgc)
Crystal Structure Of Human Peroxisomal Acetyl-Coa Acyl Transferase 1 (Acaa1)
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - 3-KETOACYL-COA THIOLASE, PEROXISOMAL
    ChainsA, B
    EC Number2.3.1.16
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPNIC28-BSA4
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneACAA1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymBETA- KETOTHIOLASE, ACETYL-COA ACYLTRANSFERASE, PEROXISOMAL 3-OXOACYL-COA THIOLASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2IIK)

(-) Sites  (0, 0)

(no "Site" information available for 2IIK)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2IIK)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2IIK)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 4)

Asymmetric/Biological Unit (2, 4)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_011904E172DTHIK_HUMANPolymorphism156265A/BE173D
2UniProtVAR_069148V387ATHIK_HUMANPolymorphism2229528A/BV388A

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

(-) PROSITE Motifs  (3, 6)

Asymmetric/Biological Unit (3, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1THIOLASE_1PS00098 Thiolases acyl-enzyme intermediate signature.THIK_HUMAN119-137
 
  2A:119-137
B:119-137
2THIOLASE_2PS00737 Thiolases signature 2.THIK_HUMAN367-383
 
  2A:368-384
B:368-384
3THIOLASE_3PS00099 Thiolases active site.THIK_HUMAN403-416
 
  2A:404-417
B:404-417

(-) Exons   (12, 24)

Asymmetric/Biological Unit (12, 24)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1bENST000003331671bENSE00001927555chr3:38178699-38178356344THIK_HUMAN1-57572A:33-57
B:21-57
25
37
1.2aENST000003331672aENSE00001317086chr3:38178176-3817808394THIK_HUMAN58-89322A:58-89
B:58-89
32
32
1.4dENST000003331674dENSE00001705640chr3:38175500-3817544358THIK_HUMAN89-108202A:89-108
B:89-108
20
20
1.6bENST000003331676bENSE00001617234chr3:38173496-3817341780THIK_HUMAN108-135282A:108-135
B:108-135
28
28
1.7ENST000003331677ENSE00001681904chr3:38173129-3817308743THIK_HUMAN135-149152A:135-149
B:135-149
15
15
1.8bENST000003331678bENSE00001600176chr3:38170879-3817078199THIK_HUMAN149-182342A:149-183 (gaps)
B:149-183 (gaps)
35
35
1.9aENST000003331679aENSE00001740629chr3:38169357-3816927781THIK_HUMAN182-209282A:183-210
B:183-210
28
28
1.10aENST0000033316710aENSE00001799097chr3:38168191-38168001191THIK_HUMAN209-273652A:210-274
B:210-274
65
65
1.10hENST0000033316710hENSE00001702141chr3:38167832-38167653180THIK_HUMAN273-333612A:274-334
B:274-334
61
61
1.10iENST0000033316710iENSE00001593720chr3:38167372-3816731756THIK_HUMAN333-351192A:334-352
B:334-352
19
19
1.11aENST0000033316711aENSE00001599475chr3:38167201-38167056146THIK_HUMAN352-400492A:353-401
B:353-401
49
49
1.11iENST0000033316711iENSE00001909066chr3:38164613-38164201413THIK_HUMAN400-424252A:401-423
B:401-425
23
25

(-) 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:386
 aligned with THIK_HUMAN | P09110 from UniProtKB/Swiss-Prot  Length:424

    Alignment length:390
                                    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       422
           THIK_HUMAN    33 ASAADVVVVHGRRTAICRAGRGGFKDTTPDELLSAVMTAVLKDVNLRPEQLGDICVGNVLQPGAGAIMARIAQFLSDIPETVPLSTVNRQCSSGLQAVASIAGGIRNGSYDIGMACGVESMSLADRGNPGNITSRLMEKEKARDCLIPMGITSENVAERFGISREKQDTFALASQQKAARAQSKGCFQAEIVPVTTTVHDDKGTKRSITVTQDEGIRPSTTMEGLAKLKPAFKKDGSTTAGNSSQVSDGAAAILLARRSKAEELGLPILGVLRSYAVVGVPPDIMGIGPAYAIPVALQKAGLTVSDVDIFEINEAFASQAAYCVEKLRLPPEKVNPLGGAVALGHPLGCTGARQVITLLNELKRRGKRAYGVVSMCIGTGMGAAAVFEYP 422
               SCOP domains d2iika1 A:33-297 automated matches                                                                                                                                                                                                                                      d2iika2 A:298-423 automated matches                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eeeeeeee...ee.........hhhhhhhhhhhhhhhhhh.hhhhh..eeee...hhhhhhhhhhhhhhhh.......eeeeehhhhhhhhhhhhhhhhhhh....eeeeeeeee.....----.....hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh........eeeeee.....eeeeee..........hhhhhhhh..................eeeeeeeeeeehhhhhhhh....eeeeeeeeee.hhhhhhhhhhhhhhhhhhhhh.hhh.eeeeee...hhhhhhhhhhhhh.hhhhh....hhhhhh....hhhhhhhhhhhhhhhhhh..eeeeeeeee...eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------D----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------A----------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------THIOLASE_1         -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------THIOLASE_2       -------------------THIOLASE_3    ------ PROSITE
           Transcript 1 (1) Exon 1.1b  PDB: A:33-57  Exon 1.2a  PDB: A:58-89         ------------------Exon 1.6b  PDB: A:108-135   -------------Exon 1.8b  PDB: A:149-183 (gaps)  --------------------------Exon 1.10a  PDB: A:210-274 UniProt: 209-273                      -----------------------------------------------------------Exon 1.10i         Exon 1.11a  PDB: A:353-401 UniProt: 352-400      ---------------------- Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------------------Exon 1.4d           --------------------------Exon 1.7       --------------------------------Exon 1.9a  PDB: A:183-210   ---------------------------------------------------------------Exon 1.10h  PDB: A:274-334 UniProt: 273-333                  ------------------------------------------------------------------Exon 1.11i [INCOMPLETE] Transcript 1 (2)
                 2iik A  33 ASAADVVVVHGRRTAICRAGRGGFKDTTPDELLSAVMTAVLKDVNLRPEQLGDICVGNVLQPGAGAIMARIAQFLSDIPETVPLSTVNRQCSSGLQAVASIAGGIRNGSYDIGMACGVESMSLAD----GNITSRLMEKEKARDCLIPMGITSENVAERFGISREKQDTFALASQQKAARAQSKGCFQAEIVPVTTTVHDDKGTKRSITVTQDEGIRPSTTMEGLAKLKPAFKKDGSTTAGNSSQVSDGAAAILLARRSKAEELGLPILGVLRSYAVVGVPPDIMGIGPAYAIPVALQKAGLTVSDVDIFEINEAFASQAAYCVEKLRLPPEKVNPLGGAVALGHPLGCTGARQVITLLNELKRRGKRAYGVVSMCIGTGMGAAAVFEYP 423
                                    42        52        62        72        82        92       102       112       122       132       142       152    |  163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423
                                                                                                                                                      157  163                                                                                                                                                                                                                                                                    

Chain B from PDB  Type:PROTEIN  Length:400
 aligned with THIK_HUMAN | P09110 from UniProtKB/Swiss-Prot  Length:424

    Alignment length:404
                                    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    
           THIK_HUMAN    21 PQAAPCLSGAPQASAADVVVVHGRRTAICRAGRGGFKDTTPDELLSAVMTAVLKDVNLRPEQLGDICVGNVLQPGAGAIMARIAQFLSDIPETVPLSTVNRQCSSGLQAVASIAGGIRNGSYDIGMACGVESMSLADRGNPGNITSRLMEKEKARDCLIPMGITSENVAERFGISREKQDTFALASQQKAARAQSKGCFQAEIVPVTTTVHDDKGTKRSITVTQDEGIRPSTTMEGLAKLKPAFKKDGSTTAGNSSQVSDGAAAILLARRSKAEELGLPILGVLRSYAVVGVPPDIMGIGPAYAIPVALQKAGLTVSDVDIFEINEAFASQAAYCVEKLRLPPEKVNPLGGAVALGHPLGCTGARQVITLLNELKRRGKRAYGVVSMCIGTGMGAAAVFEYPGN 424
               SCOP domains d2iikb1 B:21-297 automated matches                                                                                                                                                                                                                                                  d2iikb2 B:298-425 automated matches                                                                                              SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................eeeeeeee...ee.........hhhhhhhhhhhhhhhhhh.hhhhh.eeeee...hhhhhhhhhhhhhhhh.......eeeeehhhhhhhhhhhhhhhhhhh....eeeeeeeee....----......hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh........eeeeeee...eeeeeee..........hhhhhhh...................eeeeeeeeeeehhhhhhhh....eeeeeeeeee.hhhhhhhhhhhhhhhhhhhhh.hhh.eeeeee...hhhhhhhhhhhh..hhhhh..............hhhhhhhhhhhhhhhhhh..eeeeeeeee...eeeeeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------D----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------A------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------THIOLASE_1         -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------THIOLASE_2       -------------------THIOLASE_3    -------- PROSITE
           Transcript 1 (1) Exon 1.1b  PDB: B:21-57 UniProt: 1-57Exon 1.2a  PDB: B:58-89         ------------------Exon 1.6b  PDB: B:108-135   -------------Exon 1.8b  PDB: B:149-183 (gaps)  --------------------------Exon 1.10a  PDB: B:210-274 UniProt: 209-273                      -----------------------------------------------------------Exon 1.10i         Exon 1.11a  PDB: B:353-401 UniProt: 352-400      ------------------------ Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------------------------------Exon 1.4d           --------------------------Exon 1.7       --------------------------------Exon 1.9a  PDB: B:183-210   ---------------------------------------------------------------Exon 1.10h  PDB: B:274-334 UniProt: 273-333                  ------------------------------------------------------------------Exon 1.11i  PDB: B:401-42 Transcript 1 (2)
                 2iik B  21 TENLYFQSMAPQASAADVVVVHGRRTAICRAGRGGFKDTTPDELLSAVMTAVLKDVNLRPEQLGDICVGNVLQPGAGAIMARIAQFLSDIPETVPLSTVNRQCSSGLQAVASIAGGIRNGSYDIGMACGVESMSLA----PGNITSRLMEKEKARDCLIPMGITSENVAERFGISREKQDTFALASQQKAARAQSKGCFQAEIVPVTTTVHDDKGTKRSITVTQDEGIRPSTTMEGLAKLKPAFKKDGSTTAGNSSQVSDGAAAILLARRSKAEELGLPILGVLRSYAVVGVPPDIMGIGPAYAIPVALQKAGLTVSDVDIFEINEAFASQAAYCVEKLRLPPEKVNPLGGAVALGHPLGCTGARQVITLLNELKRRGKRAYGVVSMCIGTGMGAAAVFEYPGN 425
                                    30        40        50        60        70        80        90       100       110       120       130       140       150     |   -|      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       421    
                                                                                                                                                                 156  162                                                                                                                                                                                                                                                                       

   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, 4)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2IIK)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2IIK)

(-) Gene Ontology  (20, 20)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (THIK_HUMAN | P09110)
molecular function
    GO:0008775    acetate CoA-transferase activity    Catalysis of the reaction: acyl-CoA + acetate = a fatty acid anion + acetyl-CoA.
    GO:0003988    acetyl-CoA C-acyltransferase activity    Catalysis of the reaction: acyl-CoA + acetyl-CoA = CoA + 3-oxoacyl-CoA.
    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:0016401    palmitoyl-CoA oxidase activity    Catalysis of the reaction: palmitoyl-CoA + O2 = trans-2,3-dehydropalmitoyl-CoA + hydrogen peroxide.
    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: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.
    GO:0016746    transferase activity, transferring acyl groups    Catalysis of the transfer of an acyl group from one compound (donor) to another (acceptor).
    GO:0016747    transferase activity, transferring acyl groups other than amino-acyl groups    Catalysis of the transfer of an acyl group, other than amino-acyl, from one compound (donor) to another (acceptor).
biological process
    GO:0036109    alpha-linolenic acid metabolic process    The chemical reactions and pathways involving alpha-linolenic acid, an unsaturated omega-6 fatty acid that has the molecular formula C18H32O2.
    GO:0008206    bile acid metabolic process    The chemical reactions and pathways involving bile acids, any of a group of steroid carboxylic acids occurring in bile, where they are present as the sodium salts of their amides with glycine or taurine.
    GO:0006635    fatty acid beta-oxidation    A fatty acid oxidation process that results in the complete oxidation of a long-chain fatty acid. Fatty acid beta-oxidation begins with the addition of coenzyme A to a fatty acid, and occurs by successive cycles of reactions during each of which the fatty acid is shortened by a two-carbon fragment removed as acetyl coenzyme A; the cycle continues until only two or three carbons remain (as acetyl-CoA or propionyl-CoA respectively).
    GO:0033540    fatty acid beta-oxidation using acyl-CoA oxidase    A fatty acid beta-oxidation pathway in which the initial step, which converts an acyl-CoA to a trans-2-enoyl-CoA, is catalyzed by acyl-CoA oxidase; the electrons removed by oxidation pass directly to oxygen and produce hydrogen peroxide, which is cleaved by peroxisomal catalases. Fatty acid beta-oxidation begins with the addition of coenzyme A to a fatty acid, and ends when only two or three carbons remain (as acetyl-CoA or propionyl-CoA respectively).
    GO:0006631    fatty acid metabolic process    The chemical reactions and pathways involving fatty acids, aliphatic monocarboxylic acids liberated from naturally occurring fats and oils by hydrolysis.
    GO:0006629    lipid metabolic process    The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
    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:0000038    very long-chain fatty acid metabolic process    The chemical reactions and pathways involving a fatty acid which has a chain length greater than C22.
cellular component
    GO:0043231    intracellular membrane-bounded organelle    Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    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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