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(-) Description

Title :  TRUNCATED HUMAN ATP-CITRATE LYASE WITH TARTRATE BOUND
 
Authors :  M. E. Fraser, T. Sun
Date :  05 May 10  (Deposition) - 16 Jun 10  (Release) - 22 Sep 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A,B  (2x)
Keywords :  Atp-Grasp, Phosphohistidine, Organic Acid, Lyase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  T. Sun, K. Hayakawa, K. S. Bateman, M. E. Fraser
Identification Of The Citrate-Binding Site Of Human Atp-Citrate Lyase Using X-Ray Crystallography.
J. Biol. Chem. V. 285 27418 2010
PubMed-ID: 20558738  |  Reference-DOI: 10.1074/JBC.M109.078667

(-) Compounds

Molecule 1 - ATP-CITRATE SYNTHASE
    ChainsA
    EC Number2.3.3.8
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET42B+
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentTRUNCATED HUMAN ATP-CITRATE LYASE (UNP RESIDUES 1-425)
    GeneACLY
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymATP-CITRATE (PRO-S-)-LYASE, CITRATE CLEAVAGE ENZYME
 
Molecule 2 - ATP-CITRATE SYNTHASE
    ChainsB
    EC Number2.3.3.8
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET42B+
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentTRUNCATED HUMAN ATP-CITRATE LYASE (UNP RESIDUES 487-821)
    GeneACLY
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymATP-CITRATE (PRO-S-)-LYASE, CITRATE CLEAVAGE ENZYME

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
1MG1Ligand/IonMAGNESIUM ION
2TLA1Ligand/IonL(+)-TARTARIC ACID
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2TLA1Ligand/IonL(+)-TARTARIC ACID
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2TLA2Ligand/IonL(+)-TARTARIC ACID

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:257 , SER A:260 , ALA A:262 , HOH A:624BINDING SITE FOR RESIDUE MG A 426
2AC2SOFTWAREGLY A:309 , ALA A:310 , ALA A:345 , ASN A:346 , PHE A:347 , THR A:348 , ARG A:379 , HOH A:531 , HOH A:1362BINDING SITE FOR RESIDUE TLA A 427

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:20 -A:20
2A:293 -B:748

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Asn A:203 -Pro A:204
2Gly B:622 -Pro B:623

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Asymmetric Unit (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_028230E175DACLY_HUMANPolymorphism2304497AE175D

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_028230E175DACLY_HUMANPolymorphism2304497AE175D

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (1, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_028230E175DACLY_HUMANPolymorphism2304497AE175D

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

(-) PROSITE Motifs  (3, 3)

Asymmetric Unit (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SUCCINYL_COA_LIG_3PS01217 ATP-citrate lyase / succinyl-CoA ligases family signature 3.ACLY_HUMAN273-297  1A:273-297
2SUCCINYL_COA_LIG_1PS01216 ATP-citrate lyase / succinyl-CoA ligases family signature 1.ACLY_HUMAN661-690  1B:661-690
3SUCCINYL_COA_LIG_2PS00399 ATP-citrate lyase / succinyl-CoA ligases family active site.ACLY_HUMAN746-762  1B:746-751
Biological Unit 1 (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SUCCINYL_COA_LIG_3PS01217 ATP-citrate lyase / succinyl-CoA ligases family signature 3.ACLY_HUMAN273-297  1A:273-297
2SUCCINYL_COA_LIG_1PS01216 ATP-citrate lyase / succinyl-CoA ligases family signature 1.ACLY_HUMAN661-690  1B:661-690
3SUCCINYL_COA_LIG_2PS00399 ATP-citrate lyase / succinyl-CoA ligases family active site.ACLY_HUMAN746-762  1B:746-751
Biological Unit 2 (3, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SUCCINYL_COA_LIG_3PS01217 ATP-citrate lyase / succinyl-CoA ligases family signature 3.ACLY_HUMAN273-297  2A:273-297
2SUCCINYL_COA_LIG_1PS01216 ATP-citrate lyase / succinyl-CoA ligases family signature 1.ACLY_HUMAN661-690  2B:661-690
3SUCCINYL_COA_LIG_2PS00399 ATP-citrate lyase / succinyl-CoA ligases family active site.ACLY_HUMAN746-762  2B:746-751

(-) Exons   (0, 0)

(no "Exon" information available for 3MWE)

(-) 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:424
 aligned with ACLY_HUMAN | P53396 from UniProtKB/Swiss-Prot  Length:1101

    Alignment length:424
                                    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       421    
           ACLY_HUMAN     2 SAKAISEQTGKELLYKFICTTSAIQNRFKYARVTPDTDWARLLQDHPWLLSQNLVVKPDQLIKRRGKLGLVGVNLTLDGVKSWLKPRLGQEATVGKATGFLKNFLIEPFVPHSQAEEFYVCIYATREGDYVLFHHEGGVDVGDVDAKAQKLLVGVDEKLNPEDIKKHLLVHAPEDKKEILASFISGLFNFYEDLYFTYLEINPLVVTKDGVYVLDLAAKVDATADYICKVKWGDIEFPPPFGREAYPEEAYIADLDAKSGASLKLTLLNPKGRIWTMVAGGGASVVYSDTICDLGGVNELANYGEYSGAPSEQQTYDYAKTILSLMTREKHPDGKILIIGGSIANFTNVAATFKGIVRAIRDYQGPLKEHEVTIFVRRGGPNYQEGLRVMGEVGKTTGIPIHVFGTETHMTAIVGMALGHRPIP 425
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------ATP-grasp_2-3mweA01 A:29-207                                                                                                                                                       -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeehhhhhhhhhhhhh............eee....hhhhhhhhhhhhhh..eeeee.............eeeehhhhhhhhhh.....eeee..eeee...eeeee....hhh.eeeeeeeee..eeeeeee...hhhhhhhhhhheeeeee.....hhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh.eeeeeeeeeeee..eeee..eeeeee..hhhhhhhhhh............hhhhhhhhhhhhh...eeeeee......eee...hhhhhhhhhhhhhhh.hhhhh.eeeeee...hhhhhhhhhhhhhhhh........eeeee........hhhhhhhhhhhhhhhhhhhhhhh.eeeeee....hhhhhhhhhhhhhhhhh..eeee......hhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------D---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------SUCCINYL_COA_LIG_3       -------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mwe A   2 SAKAISEQTGKELLYKFICTTSAIQNRFKYARVTPDTDWARLLQDHPWLLSQNLVVKPDQLIKRRGKLGLVGVNLTLDGVKSWLKPRLGQEATVGKATGFLKNFLIEPFVPHSQAEEFYVCIYATREGDYVLFHHEGGVDVGDVDAKAQKLLVGVDEKLNPEDIKKHLLVHAPEDKKEILASFISGLFNFYEDLYFTYLEINPLVVTKDGVYVLDLAAKVDATADYICKVKWGDIEFPPPFGREAYPEEAYIADLDAKSGASLKLTLLNPKGRIWTMVAGGGASVVYSDTICDLGGVNELANYGEYSGAPSEQQTYDYAKTILSLMTREKHPDGKILIIGGSIANFTNVAATFKGIVRAIRDYQGPLKEHEVTIFVRRGGPNYQEGLRVMGEVGKTTGIPIHVFGTETHMTAIVGMALGHRPIP 425
                                    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       421    

Chain B from PDB  Type:PROTEIN  Length:320
 aligned with ACLY_HUMAN | P53396 from UniProtKB/Swiss-Prot  Length:1101

    Alignment length:335
                                   496       506       516       526       536       546       556       566       576       586       596       606       616       626       636       646       656       666       676       686       696       706       716       726       736       746       756       766       776       786       796       806       816     
           ACLY_HUMAN   487 GKSTTLFSRHTKAIVWGMQTRAVQGMLDFDYVCSRDEPSVAAMVYPFTGDHKQKFYWGHKEILIPVFKNMADAMRKHPEVDVLINFASLRSAYDSTMETMNYAQIRTIAIIAEGIPEALTRKLIKKADQKGVTIIGPATVGGIKPGCFKIGNTGGMLDNILASKLYRPGSVAYVSRSGGMSNELNNIISRTTDGVYEGVAIGGDRYPGSTFMDHVLRYQDTPGVKMIVVLGEIGGTEEYKICRGIKEGRLTKPIVCWCIGTCATMFSSEVQFGHAGACANQASETAVAKNQALKEAGVFVPRSFDELGEIIQSVYEDLVANGVIVPAQEVPPPTV 821
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------CoA_binding-3mweB01 B:494-600                                                                              -----------------------------------------------------------Ligase_CoA-3mweB02 B:660-785                                                                                                  ------------------------------------ Pfam domains
         Sec.struct. author ............eeee..hhhhhhhhhhhhhhh......eeeee......eeeeeee..eeeeeeee.hhhhhhhhh....eeee.....hhhhhhhhhh......eeee.....hhhhhhhhhhhhhhhh.eee......eee...ee......hhhhhhhh.......eeeee.hhhhhhhhhhhhhhhh..eeeeee.........hhhhhhhhhhh.....eeeeeee...hhhhhhhhhhhh......eeeeee......---------------hhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhh.............. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------SUCCINYL_COA_LIG_1            -------------------------------------------------------SUCCINYL_COA_LIG_----------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mwe B 487 GKSTTLFSRHTKAIVWGMQTRAVQGMLDFDYVCSRDEPSVAAMVYPFTGDHKQKFYWGHKEILIPVFKNMADAMRKHPEVDVLINFASLRSAYDSTMETMNYAQIRTIAIIAEGIPEALTRKLIKKADQKGVTIIGPATVGGIKPGCFKIGNTGGMLDNILASKLYRPGSVAYVSRSGGMSNELNNIISRTTDGVYEGVAIGGDRYPGSTFMDHVLRYQDTPGVKMIVVLGEIGGTEEYKICRGIKEGRLTKPIVCWCIGTCATM---------------QASETAVAKNQALKEAGVFVPRSFDELGEIIQSVYEDLVANGVIVPAQEVPPPTV 821
                                   496       506       516       526       536       546       556       566       576       586       596       606       616       626       636       646       656       666       676       686       696       706       716       726       736       746    |    -         -|      776       786       796       806       816     
                                                                                                                                                                                                                                                                                                  751             767                                                      

   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  (0, 0)

(no "SCOP Domain" information available for 3MWE)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (3, 3)

Asymmetric Unit

(-) Gene Ontology  (26, 26)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (ACLY_HUMAN | P53396)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0003878    ATP citrate synthase activity    Catalysis of the reaction: acetyl-CoA + ADP + H(+) + oxaloacetate + phosphate = ATP + citrate + 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:0048037    cofactor binding    Interacting selectively and non-covalently with a cofactor, a substance that is required for the activity of an enzyme or other protein. Cofactors may be inorganic, such as the metal atoms zinc, iron, and copper in certain forms, or organic, in which case they are referred to as coenzymes. Cofactors may either be bound tightly to active sites or bind loosely with the substrate.
    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: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:0046912    transferase activity, transferring acyl groups, acyl groups converted into alkyl on transfer    Catalysis of the transfer of an acyl group from one compound (donor) to another (acceptor), with the acyl group being converted into alkyl on transfer.
biological process
    GO:0006085    acetyl-CoA biosynthetic process    The chemical reactions and pathways resulting in the formation of acetyl-CoA, a derivative of coenzyme A in which the sulfhydryl group is acetylated.
    GO:0006084    acetyl-CoA metabolic process    The chemical reactions and pathways involving acetyl-CoA, a derivative of coenzyme A in which the sulfhydryl group is acetylated; it is a metabolite derived from several pathways (e.g. glycolysis, fatty acid oxidation, amino-acid catabolism) and is further metabolized by the tricarboxylic acid cycle. It is a key intermediate in lipid and terpenoid biosynthesis.
    GO:0006695    cholesterol biosynthetic process    The chemical reactions and pathways resulting in the formation of cholesterol, cholest-5-en-3 beta-ol, the principal sterol of vertebrates and the precursor of many steroids, including bile acids and steroid hormones.
    GO:0006101    citrate metabolic process    The chemical reactions and pathways involving citrate, 2-hydroxy-1,2,3-propanetricarboyxlate. Citrate is widely distributed in nature and is an important intermediate in the TCA cycle and the glyoxylate cycle.
    GO:0006633    fatty acid biosynthetic process    The chemical reactions and pathways resulting in the formation of a fatty acid, any of the aliphatic monocarboxylic acids that can be liberated by hydrolysis from naturally occurring fats and oils. Fatty acids are predominantly straight-chain acids of 4 to 24 carbon atoms, which may be saturated or unsaturated; branched fatty acids and hydroxy fatty acids also occur, and very long chain acids of over 30 carbons are found in waxes.
    GO:0008610    lipid biosynthetic process    The chemical reactions and pathways resulting in the formation of lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent.
    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:0035338    long-chain fatty-acyl-CoA biosynthetic process    The chemical reactions and pathways resulting in the formation of a long-chain fatty-acyl-CoA any derivative of coenzyme A in which the sulfhydryl group is in a thioester linkage with a long-chain fatty-acyl group. Long-chain fatty-acyl-CoAs have chain lengths of C13 or more.
    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: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:0031325    positive regulation of cellular metabolic process    Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances.
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:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    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)

UniProtKB/Swiss-Prot
        ACLY_HUMAN | P533963mwd 3pff

(-) Related Entries Specified in the PDB File

3mwd TRUNCATED HUMAN ATP-CITRATE LYASE WITH CITRATE BOUND