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(-) Description

Title :  LIGAND COMPLEX STRUCTURE OF SOLUBLE EPOXIDE HYDROLASE
 
Authors :  L. Oster, S. Tapani, Y. Xue, H. Kack
Date :  02 Mar 15  (Deposition) - 13 May 15  (Release) - 23 Sep 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.15
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Oster, S. Tapani, Y. Xue, H. Kack
Successful Generation Of Structural Information For Fragment-Based Drug Discovery.
Drug Discov Today V. 20 1104 2015
PubMed-ID: 25931264  |  Reference-DOI: 10.1016/J.DRUDIS.2015.04.005

(-) Compounds

Molecule 1 - BIFUNCTIONAL EPOXIDE HYDROLASE 2
    Chains: A
    EC Number: 3.3.2.10, 3.1.3.76
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Cell Line: SF9
    Expression System Common: FALL ARMYWORM
    Expression System Taxid: 7108
    Expression System Vector Type: BACULOVIRUS
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: EPOXIDE HYDRATASE, SOLUBLE EPOXIDE HYDROLASE, SEH

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 8)

Asymmetric Unit (4, 8)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2PEG2Ligand/IonDI(HYDROXYETHYL)ETHER
3SO42Ligand/IonSULFATE ION
4YPN3Ligand/Ion2-[(5-CHLORO-2-PYRIDYL)SULFANYL]ETHANOL
Biological Unit 1 (4, 16)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2PEG4Ligand/IonDI(HYDROXYETHYL)ETHER
3SO44Ligand/IonSULFATE ION
4YPN6Ligand/Ion2-[(5-CHLORO-2-PYRIDYL)SULFANYL]ETHANOL

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:228 , ARG A:440 , MET A:441 , VAL A:442 , THR A:443 , GLU A:446 , HOH A:2168BINDING SITE FOR RESIDUE SO4 A1548
2AC2SOFTWARELYS A:144 , MET A:145 , PHE A:147 , HOH A:2078BINDING SITE FOR RESIDUE SO4 A1549
3AC3SOFTWARETHR A:532 , ASN A:535 , GLN A:536 , ILE A:539 , LYS A:540 , HOH A:2323 , HOH A:2333 , HOH A:2334BINDING SITE FOR RESIDUE PEG A1550
4AC4SOFTWAREPRO A:371 , SER A:374 , ILE A:375 , ASN A:378 , YPN A:1555BINDING SITE FOR RESIDUE PEG A1551
5AC5SOFTWARECYS A:141 , ALA A:282 , GLY A:325 , SER A:327 , HOH A:2148BINDING SITE FOR RESIDUE GOL A1552
6AC6SOFTWAREASP A:335 , TRP A:336 , TYR A:383 , GLN A:384 , TYR A:466 , YPN A:1555 , HOH A:2159BINDING SITE FOR RESIDUE YPN A1553
7AC7SOFTWARETYR A:383 , LEU A:408 , ARG A:410 , SER A:415 , ASP A:496 , VAL A:498 , HIS A:524 , TRP A:525 , HOH A:2242 , HOH A:2303BINDING SITE FOR RESIDUE YPN A1554
8AC8SOFTWAREMET A:339 , LEU A:499 , PEG A:1551 , YPN A:1553 , HOH A:2276BINDING SITE FOR RESIDUE YPN A1555

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5AK6)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Leu A:16 -Pro A:17
2Lys A:160 -Pro A:161
3Phe A:267 -Pro A:268

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5AK6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5AK6)

(-) Exons   (0, 0)

(no "Exon" information available for 5AK6)

(-) 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:541
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee......ee..hhhhhhhhhhhh....hhhhhhhh.....hhhhhhhh...hhhhhhhhhhhhhhhhh......hhhhhhhhhhhhheehhhhhhhhhhhhhh..eeeeee.........hhhhhhhhhhhhh...eeeehhhhh....hhhhhhhhhhhhh.hhh.eeeee.hhhhhhhhhhh..eeee..hhhhhhhhhhhhhh..............hhhhheeeeeeee..eeeeeeee....eeeee.....hhhhhh.hhhhhhhh..eeeee............hhhhhhhhhhhhhhhhhhhhhh...eeeeeehhhhhhhhhhhhhh...eeeeeee...........hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh...........hhhhhh................hhhhhhhhhhhhhh..hhhhhhh..hhhhhhhhhhhhh.......eeeeee......hhhhhhhhhhh....eeeee.....hhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ak6 A   2 TLRAAVFDLDGVLALPAVFGVLGRTEEALALPRGLLNDAFQKGGPEGATTRLMKGEITLSQWIPLMEENCRKCSCLPKNFSIKEIFDKAISARKINRPMLQAALMLRKKGFTTAILTNTWLDDRAERDGLAQLMCELKMHFDFLIESCQVGMVKPEPQIYKFLLDTLKASPSEVVFLDDIGANLKPARDLGMVTILVQDTDTALKELEKVTGIQLLNTPAPLPTSCNPSDMSHGYVTVKPRVRLHFVELGSGPAVCLCHGFPESWYSWRYQIPALAQAGYRVLAMDMKGYGESSAPPEIEEYCMEVLCKEMVTFLDKLGLSQAVFIGHDWGGMLVWYMALFYPERVRAVASLNTPFIPANPNMSPLESIKANPVFDYQLYFQEPGVAEAELEQNLSRTFKSLFRASDESVLSMHKVCEAGGLFVNSPEEPSLSRMVTEEEIQFYVQQFKKSGFRGPLNWYRNMERNWKWACKSLGRKILIPALMVTAEKDFVLVPQMSQHMEDWIPHLKRGHIEDCGHWTQMDKPTEVNQILIKWLDSDAR 547
                                    11        21        31        41        51        61        71   ||   86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546 
                                                                                                    75|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
                                                                                                     81
   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 5AK6)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5AK6)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5AK6)

(-) Gene Ontology  (32, 32)

Asymmetric Unit(hide GO term definitions)

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  3.1.3.76
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        HYES_HUMAN | P34913: 1s8o 1vj5 1zd2 1zd3 1zd4 1zd5 3ans 3ant 3i1y 3i28 3koo 3otq 3pdc 3wk4 3wk5 3wk6 3wk7 3wk8 3wk9 3wka 3wkb 3wkc 3wkd 3wke 4c4x 4c4y 4c4z 4hai 4j03 4jnc 4ocz 4od0 4x6x 4x6y 4y2j 4y2p 4y2q 4y2r 4y2s 4y2t 4y2u 4y2v 4y2x 4y2y 5ahx 5ai0 5ai4 5ai5 5ai6 5ai8 5ai9 5aia 5aib 5aic 5ak3 5ak4 5ak5 5ake 5akg 5akh 5aki 5akj 5akk 5akl 5akx 5aky 5akz 5ald 5ale 5alf 5alg 5alh 5ali 5alj 5alk 5all 5alm 5aln 5alo 5alp 5alq 5alr 5als 5alt 5alu 5alv 5alw 5alx 5aly 5alz 5am0 5am1 5am2 5am3 5am4 5am5 5fp0

(-) Related Entries Specified in the PDB File

5ak3 LIGAND COMPLEX STRUCTURE OF SOLUBLE EPOXIDE HYDROLASE
5ak4 LIGAND COMPLEX STRUCTURE OF SOLUBLE EPOXIDE HYDROLASE
5ak5 LIGAND COMPLEX STRUCTURE OF SOLUBLE EPOXIDE HYDROLASE
5ake LIGAND COMPLEX STRUCTURE OF SOLUBLE EPOXIDE HYDROLASE
5akg LIGAND COMPLEX STRUCTURE OF SOLUBLE EPOXIDE HYDROLASE
5akh LIGAND COMPLEX STRUCTURE OF SOLUBLE EPOXIDE HYDROLASE
5aki LIGAND COMPLEX STRUCTURE OF SOLUBLE EPOXIDE HYDROLASE
5akj LIGAND COMPLEX STRUCTURE OF SOLUBLE EPOXIDE HYDROLASE
5akk LIGAND COMPLEX STRUCTURE OF SOLUBLE EPOXIDE HYDROLASE
5akl LIGAND COMPLEX STRUCTURE OF SOLUBLE EPOXIDE HYDROLASE
5akx LIGAND COMPLEX STRUCTURE OF SOLUBLE EPOXIDE HYDROLASE
5aky LIGAND COMPLEX STRUCTURE OF SOLUBLE EPOXIDE HYDROLASE
5akz LIGAND COMPLEX STRUCTURE OF SOLUBLE EPOXIDE HYDROLASE
5ald LIGAND COMPLEX STRUCTURE OF SOLUBLE EPOXIDE HYDROLASE
5ale LIGAND COMPLEX STRUCTURE OF SOLUBLE EPOXIDE HYDROLASE
5alf LIGAND COMPLEX STRUCTURE OF SOLUBLE EPOXIDE HYDROLASE
5alg LIGAND COMPLEX STRUCTURE OF SOLUBLE EPOXIDE HYDROLASE
5alh LIGAND COMPLEX STRUCTURE OF SOLUBLE EPOXIDE HYDROLASE
5ali LIGAND COMPLEX STRUCTURE OF SOLUBLE EPOXIDE HYDROLASE
5alj LIGAND COMPLEX STRUCTURE OF SOLUBLE EPOXIDE HYDROLASE
5alk LIGAND COMPLEX STRUCTURE OF SOLUBLE EPOXIDE HYDROLASE
5all LIGAND COMPLEX STRUCTURE OF SOLUBLE EPOXIDE HYDROLASE
5alm LIGAND COMPLEX STRUCTURE OF SOLUBLE EPOXIDE HYDROLASE
5aln LIGAND COMPLEX STRUCTURE OF SOLUBLE EPOXIDE HYDROLASE
5alo LIGAND COMPLEX STRUCTURE OF SOLUBLE EPOXIDE HYDROLASE
5alp LIGAND COMPLEX STRUCTURE OF SOLUBLE EPOXIDE HYDROLASE
5alq LIGAND COMPLEX STRUCTURE OF SOLUBLE EPOXIDE HYDROLASE
5alr LIGAND COMPLEX STRUCTURE OF SOLUBLE EPOXIDE HYDROLASE
5als LIGAND COMPLEX STRUCTURE OF SOLUBLE EPOXIDE HYDROLASE
5alt LIGAND COMPLEX STRUCTURE OF SOLUBLE EPOXIDE HYDROLASE
5alu LIGAND COMPLEX STRUCTURE OF SOLUBLE EPOXIDE HYDROLASE
5alv LIGAND COMPLEX STRUCTURE OF SOLUBLE EPOXIDE HYDROLASE
5alw LIGAND COMPLEX STRUCTURE OF SOLUBLE EPOXIDE HYDROLASE
5alx LIGAND COMPLEX STRUCTURE OF SOLUBLE EPOXIDE HYDROLASE
5aly LIGAND COMPLEX STRUCTURE OF SOLUBLE EPOXIDE HYDROLASE
5alz LIGAND COMPLEX STRUCTURE OF SOLUBLE EPOXIDE HYDROLASE
5am0 LIGAND COMPLEX STRUCTURE OF SOLUBLE EPOXIDE HYDROLASE
5am1 LIGAND COMPLEX STRUCTURE OF SOLUBLE EPOXIDE HYDROLASE
5am2 LIGAND COMPLEX STRUCTURE OF SOLUBLE EPOXIDE HYDROLASE
5am3 LIGAND COMPLEX STRUCTURE OF SOLUBLE EPOXIDE HYDROLASE
5am4 LIGAND COMPLEX STRUCTURE OF SOLUBLE EPOXIDE HYDROLASE
5am5 LIGAND COMPLEX STRUCTURE OF SOLUBLE EPOXIDE HYDROLASE