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(-) Description

Title :  HUMAN S-ADENOSYLHOMOCYSTEINE HYDROLASE COMPLEXED WITH NEPLANOCIN
 
Authors :  X. Yang, Y. Hu, D. H. Yin, M. A. Turner, M. Wang, R. T. Borchardt, P. L. Howe K. Kuczera, R. L. Schowen
Date :  17 Apr 02  (Deposition) - 20 May 03  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.01
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (4x)
Keywords :  Alpha-Beta Structure, Inhibitor Complex, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  X. Yang, Y. Hu, D. H. Yin, M. A. Turner, M. Wang, R. T. Borchardt, P. L. Howell, K. Kuczera, R. L. Schowen
Catalytic Strategy Of S-Adenosyl-L-Homocysteine Hydrolase: Transition-State Stabilization And The Avoidance Of Abortiv Reactions
Biochemistry V. 42 1900 2003
PubMed-ID: 12590576  |  Reference-DOI: 10.1021/BI0262350

(-) Compounds

Molecule 1 - S-ADENOSYLHOMOCYSTEINE HYDROLASE
    ChainsA
    EC Number3.3.1.1
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPPROKCD20
    Expression System Taxid562
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (4x)A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric Unit (3, 4)
No.NameCountTypeFull Name
1IPA2Ligand/IonISOPROPYL ALCOHOL
2NAD1Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
3NOC1Ligand/Ion3-(6-AMINO-PURIN-9-YL)-5-HYDROXYMETHYL-CYCLOPENTANE-1,2-DIOL
Biological Unit 1 (3, 16)
No.NameCountTypeFull Name
1IPA8Ligand/IonISOPROPYL ALCOHOL
2NAD4Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
3NOC4Ligand/Ion3-(6-AMINO-PURIN-9-YL)-5-HYDROXYMETHYL-CYCLOPENTANE-1,2-DIOL

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:157 , THR A:158 , THR A:159 , ASP A:190 , ASN A:191 , GLY A:220 , GLY A:222 , ASP A:223 , VAL A:224 , THR A:242 , GLU A:243 , ILE A:244 , ASP A:245 , ASN A:248 , THR A:275 , THR A:276 , CYS A:278 , ILE A:281 , ILE A:299 , GLY A:300 , HIS A:301 , LEU A:344 , ASN A:346 , HIS A:353 , LYS A:426 , TYR A:430 , NOC A:434 , HOH A:903 , HOH A:929 , HOH A:930 , HOH A:938 , HOH A:998BINDING SITE FOR RESIDUE NAD A 433
2AC2SOFTWAREHIS A:55 , THR A:57 , GLU A:59 , THR A:60 , ASP A:131 , GLU A:156 , THR A:157 , LYS A:186 , ASP A:190 , HIS A:301 , MET A:351 , GLY A:352 , HIS A:353 , MET A:358 , PHE A:362 , NAD A:433BINDING SITE FOR RESIDUE NOC A 434
3AC3SOFTWAREARG A:238 , ALA A:253 , TYR A:257 , VAL A:259 , LEU A:402 , HOH A:1039BINDING SITE FOR RESIDUE IPA A 900
4AC4SOFTWAREGLN A:85 , ASP A:86 , HIS A:87BINDING SITE FOR RESIDUE IPA A 901

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1LI4)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Gly A:423 -Pro A:424

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (6, 6)

Asymmetric Unit (6, 6)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_052286R38WSAHH_HUMANPolymorphism13043752AR38W
2UniProtVAR_058588R49CSAHH_HUMANDisease (HMAHCHD)369428934AR49C
3UniProtVAR_058589D86GSAHH_HUMANDisease (HMAHCHD)773162208AD86G
4UniProtVAR_006934D86NSAHH_HUMANPolymorphism  ---AD86N
5UniProtVAR_058590A89VSAHH_HUMANDisease (HMAHCHD)755222515AA89V
6UniProtVAR_058591Y143CSAHH_HUMANDisease (HMAHCHD)121918608AY143C

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (6, 24)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_052286R38WSAHH_HUMANPolymorphism13043752AR38W
2UniProtVAR_058588R49CSAHH_HUMANDisease (HMAHCHD)369428934AR49C
3UniProtVAR_058589D86GSAHH_HUMANDisease (HMAHCHD)773162208AD86G
4UniProtVAR_006934D86NSAHH_HUMANPolymorphism  ---AD86N
5UniProtVAR_058590A89VSAHH_HUMANDisease (HMAHCHD)755222515AA89V
6UniProtVAR_058591Y143CSAHH_HUMANDisease (HMAHCHD)121918608AY143C

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

(-) PROSITE Motifs  (2, 2)

Asymmetric Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ADOHCYASE_1PS00738 S-adenosyl-L-homocysteine hydrolase signature 1.SAHH_HUMAN78-92  1A:78-92
2ADOHCYASE_2PS00739 S-adenosyl-L-homocysteine hydrolase signature 2.SAHH_HUMAN213-229  1A:213-229
Biological Unit 1 (2, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ADOHCYASE_1PS00738 S-adenosyl-L-homocysteine hydrolase signature 1.SAHH_HUMAN78-92  4A:78-92
2ADOHCYASE_2PS00739 S-adenosyl-L-homocysteine hydrolase signature 2.SAHH_HUMAN213-229  4A:213-229

(-) Exons   (10, 10)

Asymmetric Unit (10, 10)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000002174261aENSE00001152081chr20:32891154-32891049106SAHH_HUMAN1-10101A:3-108
1.4bENST000002174264bENSE00000860101chr20:32883391-32883201191SAHH_HUMAN10-73641A:10-7364
1.5ENST000002174265ENSE00000661390chr20:32881962-3288188776SAHH_HUMAN74-99261A:74-9926
1.6ENST000002174266ENSE00000661389chr20:32880313-32880164150SAHH_HUMAN99-149511A:99-14951
1.7bENST000002174267bENSE00000661388chr20:32879337-32879225113SAHH_HUMAN149-186381A:149-18638
1.8ENST000002174268ENSE00000661387chr20:32878744-32878537208SAHH_HUMAN187-256701A:187-25670
1.9aENST000002174269aENSE00000661386chr20:32878444-3287835788SAHH_HUMAN256-285301A:256-28530
1.9cENST000002174269cENSE00001048932chr20:32878255-32878138118SAHH_HUMAN285-324401A:285-32440
1.10ENST0000021742610ENSE00000661384chr20:32873440-32873246195SAHH_HUMAN325-389651A:325-38965
1.11bENST0000021742611bENSE00001820276chr20:32868971-32868074898SAHH_HUMAN390-432431A:390-43243

(-) 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:430
 aligned with SAHH_HUMAN | P23526 from UniProtKB/Swiss-Prot  Length:432

    Alignment length:430
                                    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       332       342       352       362       372       382       392       402       412       422       432
           SAHH_HUMAN     3 DKLPYKVADIGLAAWGRKALDIAENEMPGLMRMRERYSASKPLKGARIAGCLHMTVETAVLIETLVTLGAEVQWSSCNIFSTQDHAAAAIAKAGIPVYAWKGETDEEYLWCIEQTLYFKDGPLNMILDDGGDLTNLIHTKYPQLLPGIRGISEETTTGVHNLYKMMANGILKVPAINVNDSVTKSKFDNLYGCRESLIDGIKRATDVMIAGKVAVVAGYGDVGKGCAQALRGFGARVIITEIDPINALQAAMEGYEVTTMDEACQEGNIFVTTTGCIDIILGRHFEQMKDDAIVCNIGHFDVEIDVKWLNENAVEKVNIKPQVDRYRLKNGRRIILLAEGRLVNLGCAMGHPSFVMSNSFTNQVMAQIELWTHPDKYPVGVHFLPKKLDEAVAEAHLGKLNVKLTKLTEKQAQYLGMSCDGPFKPDHYRY 432
               SCOP domains d1li4a2 A:3-189,A:353-432 S-adenosylhomocystein hydrolase                                                                                                                                  d1li4a1 A:190-352 S-adenosylhomocystein hydrolase                                                                                                                  d1li4a2 A:3-189,A:353-432 S-adenosylhomocystein hydrolase                        SCOP domains
               CATH domains 1li4A01 A:3-192,A:353-404  [code=3.40.50.1480, no name defined]                                                                                                                               1li4A02 A:193-352 NAD(P)-binding Rossmann-like Domain                                                                                                           1li4A01 A:3-192,A:353-404                           ---------------------------- CATH domains
           Pfam domains (1) --AdoHcyase-1li4A01 A:5-431                                                                                                                                                                                                                                                                                                                                                                                                                  - Pfam domains (1)
           Pfam domains (2) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AdoHcyase_NAD-1li4A02 A:191-352                                                                                                                                   -------------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author .....ee.hhhhhhhhhhhhhhhhh.hhhhhhhhhhhh........eeeee...hhhhhhhhhhhhhh..eeeee.......hhhhhhhhhhh...eee....hhhhhhhhhhh..ee..ee..eeee..hhhhhhhhhhhhhhhhhh.eeee.hhhhhhhhhhhhhh.....eeee...hhhhhhhhhhhhhhhhhhhhhhhhhh......eeeee..hhhhhhhhhhhhhh..eeeee..hhhhhhhhhhh..ee.hhhhhh....eeee........hhhhhh.....eeeee........hhhhhhhhh.eeeeee..eeeee.....eeeee.hhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhh..eee..hhhhhhhhhhhhhh.........hhhhhhhhh.............. Sec.struct. author
             SAPs(SNPs) (1) -----------------------------------W----------C------------------------------------G--V-----------------------------------------------------C------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) -----------------------------------------------------------------------------------N---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (2)
                    PROSITE ---------------------------------------------------------------------------ADOHCYASE_1    ------------------------------------------------------------------------------------------------------------------------ADOHCYASE_2      ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) 1.1a    ---------------------------------------------------------------Exon 1.5  PDB: A:74-99    -------------------------------------------------Exon 1.7b  PDB: A:149-186             Exon 1.8  PDB: A:187-256 UniProt: 187-256                             ----------------------------Exon 1.9c  PDB: A:285-324               Exon 1.10  PDB: A:325-389 UniProt: 325-389                       Exon 1.11b  PDB: A:390-432 UniProt: 390-432 Transcript 1 (1)
           Transcript 1 (2) -------Exon 1.4b  PDB: A:10-73 UniProt: 10-73                          -------------------------Exon 1.6  PDB: A:99-149 UniProt: 99-149            ----------------------------------------------------------------------------------------------------------Exon 1.9a  PDB: A:256-285     --------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 1li4 A   3 DKLPYKVADIGLAAWGRKALDIAENEMPGLMRMRERYSASKPLKGARIAGCLHMTVETAVLIETLVTLGAEVQWSSCNIFSTQDHAAAAIAKAGIPVYAWKGETDEEYLWCIEQTLYFKDGPLNMILDDGGDLTNLIHTKYPQLLPGIRGISEETTTGVHNLYKMMANGILKVPAINVNDSVTKSKFDNLYGCRESLIDGIKRATDVMIAGKVAVVAGYGDVGKGCAQALRGFGARVIITEIDPINALQAAMEGYEVTTMDEACQEGNIFVTTTGCIDIILGRHFEQMKDDAIVCNIGHFDVEIDVKWLNENAVEKVNIKPQVDRYRLKNGRRIILLAEGRLVNLGCAMGHPSFVMSNSFTNQVMAQIELWTHPDKYPVGVHFLPKKLDEAVAEAHLGKLNVKLTKLTEKQAQYLGMSCDGPFKPDHYRY 432
                                    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       332       342       352       362       372       382       392       402       412       422       432

   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  (2, 2)

Asymmetric Unit

(-) CATH Domains  (2, 2)

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

(-) Pfam Domains  (2, 2)

Asymmetric Unit

(-) Gene Ontology  (22, 22)

Asymmetric Unit(hide GO term definitions)
Chain A   (SAHH_HUMAN | P23526)
molecular function
    GO:0051287    NAD binding    Interacting selectively and non-covalently with nicotinamide adenine dinucleotide, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NAD+, or the reduced form, NADH.
    GO:0004013    adenosylhomocysteinase activity    Catalysis of the reaction: S-adenosyl-L-homocysteine + H2O = adenosine + L-homocysteine.
    GO:0030554    adenyl nucleotide binding    Interacting selectively and non-covalently with adenyl nucleotides, any compound consisting of adenosine esterified with (ortho)phosphate.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    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).
biological process
    GO:0019510    S-adenosylhomocysteine catabolic process    The chemical reactions and pathways resulting in the breakdown of S-adenosylhomocysteine, forming homocysteine and then methionine.
    GO:0033353    S-adenosylmethionine cycle    A cyclic series of interconversions involving S-adenosylmethionine, S-adenosyl-L-homocysteine, L-cysteine, and L-methionine. Couples utilization of the methyl group of SAM with recycling of the homocysteinyl group and regeneration of methionine.
    GO:0002439    chronic inflammatory response to antigenic stimulus    A chronic inflammatory response to an antigenic stimulus. A chronic inflammatory response persists indefinitely during days, weeks, or months in the life of an individual.
    GO:0042745    circadian sleep/wake cycle    The cycle from wakefulness through an orderly succession of sleep states and stages that occurs on an approximately 24 hour rhythm.
    GO:0071268    homocysteine biosynthetic process    The chemical reactions and pathways resulting in the formation of homocysteine, 2-amino-4-sulfanylbutanoic acid.
    GO:0032259    methylation    The process in which a methyl group is covalently attached to a molecule.
    GO:0006730    one-carbon metabolic process    The chemical reactions and pathways involving the transfer of one-carbon units in various oxidation states.
    GO:0001666    response to hypoxia    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 stimulus indicating lowered oxygen tension. Hypoxia, defined as a decline in O2 levels below normoxic levels of 20.8 - 20.95%, results in metabolic adaptation at both the cellular and organismal level.
    GO:0007584    response to nutrient    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 nutrient stimulus.
    GO:0000096    sulfur amino acid metabolic process    The chemical reactions and pathways involving amino acids containing sulfur, comprising cysteine, homocysteine, methionine and selenocysteine.
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:0042470    melanosome    A tissue-specific, membrane-bounded cytoplasmic organelle within which melanin pigments are synthesized and stored. Melanosomes are synthesized in melanocyte cells.
    GO:0043005    neuron projection    A prolongation or process extending from a nerve cell, e.g. an axon or dendrite.
    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)

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        SAHH_HUMAN | P235261a7a 3nj4 4pfj 4pgf 4yvf 5w49 5w4b

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