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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN HALOACID DEHALOGENASE-LIKE HYDROLASE DOMAIN CONTAINING 3 (HDHD3)
 
Authors :  E. Ugochukwu, K. Guo, W. W. Yue, E. Pilka, S. Picaud, J. Muniz, A. C. W. Pik T. Krojer, M. Gomes, F. Von Delft, C. Bountra, C. H. Arrowsmith, J. Wei A. Edwards, K. Kavanagh, U. Oppermann, Structural Genomics Consor (Sgc)
Date :  29 Sep 09  (Deposition) - 03 Nov 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.55
Chains :  Asym./Biol. Unit :  A
Keywords :  Hdhd3, Haloacid Dehalogenase-Like Hydrolase Domain Containing 3, Structural Genomics, Structural Genomics Consortium, Sgc, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Ugochukwu, K. Guo, W. W. Yue, E. Pilka, K. Kavanagh, U. Oppermann
Crystal Structure Of Human Haloacid Dehalogenase-Like Hydrolase Domain Containing 3 (Hdhd3)
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - HALOACID DEHALOGENASE-LIKE HYDROLASE DOMAIN-CONTAINING PROTEIN 3
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PNIC-CTHF
    Expression System Strain: BL21(DE3)-R3
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: HDHD3
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric/Biological Unit (3, 5)
No.NameCountTypeFull Name
1EDO1Ligand/Ion1,2-ETHANEDIOL
2GOL1Ligand/IonGLYCEROL
3MSE3Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:63 , TRP A:75 , PHE A:137 , ASP A:138 , HOH A:397BINDING SITE FOR RESIDUE EDO A 2
2AC2SOFTWARETYR A:29 , TRP A:75 , LEU A:101 , TYR A:102 , PHE A:105 , ARG A:140BINDING SITE FOR RESIDUE GOL A 3

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3K1Z)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Lys A:167 -Pro A:168

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Asymmetric/Biological Unit (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_032298G146EHDHD3_HUMANPolymorphism1043836AG146E
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3K1Z)

(-) Exons   (0, 0)

(no "Exon" information available for 3K1Z)

(-) 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:241
 aligned with HDHD3_HUMAN | Q9BSH5 from UniProtKB/Swiss-Prot  Length:251

    Alignment length:241
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246 
          HDHD3_HUMAN     7 IRLLTWDVKDTLLRLRHPLGEAYATKARAHGLEVEPSALEQGFRQAYRAQSHSFPNYGLSHGLTSRQWWLDVVLQTFHLAGVQDAQAVAPIAEQLYKDFSHPCTWQVLDGAEDTLRECRTRGLRLAVISNFDRRLEGILGGLGLREHFDFVLTSEAAGWPKPDPRIFQEALRLAHMEPVVAAHVGDNYLCDYQGPRAVGMHSFLVVGPQALDPVVRDSVPKEHILPSLAHLLPALDCLEGS 247
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---HAD_2-3k1zA01 A:10-211                                                                                                                                                                                    ------------------------------------ Pfam domains
         Sec.struct. author ..eeee......eee..hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh.eee..hhhhhhhhhhhh..eeeeee....hhhhhhhhh.hhhhh..eeehhhhh....hhhhhhhhhhhhh.hhh.eeeee.hhhhhhhhhhh...eeeee......hhhhhhhhhhh.ee.hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------E----------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3k1z A   7 mRLLTWDVKDTLLRLRHPLGEAYATKARAHGLEVEPSALEQGFRQAYRAQSHSFPNYGLSHGLTSRQWWLDVVLQTFHLAGVQDAQAVAPIAEQLYKDFSHPCTWQVLDGAEDTLRECRTRGLRLAVISNFDRRLEGILGGLGLREHFDFVLTSEAAGWPKPDPRIFQEALRLAHmEPVVAAHVGDNYLCDYQGPRAVGmHSFLVVGPQALDPVVRDSVPKEHILPSLAHLLPALDCLEGS 247
                            |       16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176     | 186       196       206       216       226       236       246 
                            |                                                                                                                                                                            182-MSE                 206-MSE                                     
                            7-MSE
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  - → Gap (green background, '-', border residues have a numbering label)
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  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 3K1Z)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3K1Z)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: HAD (186)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (HDHD3_HUMAN | Q9BSH5)
molecular function
    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: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: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.
cellular component
    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.

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 Related Entries

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(-) Related Entries Specified in the PDB File

2w4m THE CRYSTAL STRUCTURE OF HUMAN N-ACETYLNEURAMINIC ACID PHOSPHATASE, NANP
3hlt THE CRYSTAL STRUCTURE OF HUMAN HALOACID DEHALOGENASE-LIKE HYDROLASE DOMAIN CONTAINING 2 (HDHD2)