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(-) Description

Title :  CRYSTAL STRUCTURE OF LEUKOTRIENE A4 HYDROLASE IN COMPLEX WITH 4-AMINO-N-[4-(PHENYLMETHOXY)PHENYL]-BUTANAMIDE
 
Authors :  M. M. G. M. Thunnissen, M. Adler, M. Whitlow
Date :  10 Mar 08  (Deposition) - 22 Apr 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A
Keywords :  Epoxide Hydrolase, Alpha-Beta Protein, Leukotriene Biosynthesis, Metalloprotease, Inhibitor Complex, Alternative Splicing, Cytoplasm, Metal-Binding, Multifunctional Enzyme, Zinc (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  T. A. Kirkland, M. Adler, J. G. Bauman, M. Chen, J. Z. Haeggstrom, B. King, M. J. Kochanny, A. M. Liang, L. Mendoza, G. B. Phillips, M. Thunnissen, L. Trinh, M. Whitlow, B. Ye, H. Ye, J. Parkinson, W. J. Guilford
Synthesis Of Glutamic Acid Analogs As Potent Inhibitors Of Leukotriene A4 Hydrolase.
Bioorg. Med. Chem. V. 16 4963 2008
PubMed-ID: 18394906  |  Reference-DOI: 10.1016/J.BMC.2008.03.042
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - LEUKOTRIENE A-4 HYDROLASE
    ChainsA
    EC Number3.3.2.6
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPT3-MB4
    Expression System StrainJM101
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneLTA4H, LTA4
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymLTA-4 HYDROLASE, LEUKOTRIENE A(4) HYDROLASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (4, 4)
No.NameCountTypeFull Name
14BS1Ligand/Ion4-AMINO-N-[4-(BENZYLOXY)PHENYL]BUTANAMIDE
2IMD1Ligand/IonIMIDAZOLE
3YB1Ligand/IonYTTERBIUM (III) ION
4ZN1Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:295 , HIS A:299 , GLU A:318 , HOH A:627BINDING SITE FOR RESIDUE ZN A 611
2AC2SOFTWAREASP A:422 , ASP A:426 , ASP A:481 , HOH A:631 , HOH A:749BINDING SITE FOR RESIDUE YB A 612
3AC3SOFTWAREGLN A:136 , GLY A:269 , GLU A:271 , TRP A:311 , PHE A:314 , GLU A:318 , PRO A:374 , ALA A:377 , TYR A:378BINDING SITE FOR RESIDUE 4BS A 613
4AC4SOFTWAREGLY A:344 , GLY A:347 , GLU A:348 , GLU A:501 , ALA A:504 , GLN A:508BINDING SITE FOR RESIDUE IMD A 614

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Gln A:136 -Ala A:137
2Ala A:510 -Pro A:511

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Asymmetric/Biological Unit (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_051570Y131HLKHA4_HUMANPolymorphism45630737AY130H

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZINC_PROTEASEPS00142 Neutral zinc metallopeptidases, zinc-binding region signature.LKHA4_HUMAN293-302  1A:292-301

(-) Exons   (19, 19)

Asymmetric/Biological Unit (19, 19)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.2ENST000002287402ENSE00000817988chr12:96429365-96429139227LKHA4_HUMAN1-53531A:1-5252
1.3ENST000002287403ENSE00000753490chr12:96422963-96422833131LKHA4_HUMAN54-97441A:53-9644
1.4ENST000002287404ENSE00000753489chr12:96421342-96421222121LKHA4_HUMAN97-137411A:96-13641
1.5ENST000002287405ENSE00000753488chr12:96418325-9641825769LKHA4_HUMAN138-160231A:137-15923
1.6ENST000002287406ENSE00000753487chr12:96416029-96415925105LKHA4_HUMAN161-195351A:160-19435
1.7ENST000002287407ENSE00000753486chr12:96414915-9641486353LKHA4_HUMAN196-213181A:195-21218
1.9ENST000002287409ENSE00000753485chr12:96413018-9641294673LKHA4_HUMAN213-237251A:212-23625
1.10ENST0000022874010ENSE00000817987chr12:96412681-96412541141LKHA4_HUMAN238-284471A:237-28347
1.11ENST0000022874011ENSE00000994202chr12:96411358-9641133524LKHA4_HUMAN285-29281A:284-2918
1.12ENST0000022874012ENSE00000753483chr12:96410892-9641082271LKHA4_HUMAN293-316241A:292-31524
1.13ENST0000022874013ENSE00000753482chr12:96409472-96409361112LKHA4_HUMAN316-353381A:315-35238
1.14ENST0000022874014ENSE00000753481chr12:96408777-96408633145LKHA4_HUMAN354-402491A:353-40149
1.15ENST0000022874015ENSE00000753480chr12:96407631-96407528104LKHA4_HUMAN402-436351A:401-43535
1.16ENST0000022874016ENSE00000753478chr12:96407036-9640696671LKHA4_HUMAN437-460241A:436-45924
1.17ENST0000022874017ENSE00000753477chr12:96402926-9640287255LKHA4_HUMAN460-478191A:459-47719
1.18ENST0000022874018ENSE00000753476chr12:96400187-9640009296LKHA4_HUMAN479-510321A:478-50932
1.19ENST0000022874019ENSE00000753475chr12:96397698-9639761683LKHA4_HUMAN511-538281A:510-53728
1.20ENST0000022874020ENSE00001627094chr12:96396842-96396738105LKHA4_HUMAN538-573361A:537-57236
1.21ENST0000022874021ENSE00001640843chr12:96394884-96394611274LKHA4_HUMAN573-611391A:572-61039

(-) 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:610
 aligned with LKHA4_HUMAN | P09960 from UniProtKB/Swiss-Prot  Length:611

    Alignment length:610
                                    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       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591       601       611
          LKHA4_HUMAN     2 PEIVDTCSLASPASVCRTKHLHLRCSVDFTRRTLTGTAALTVQSQEDNLRSLVLDTKDLTIEKVVINGQEVKYALGERQSYKGSPMEISLPIALSKNQEIVIEISFETSPKSSALQWLTPEQTSGKEHPYLFSQCQAIHCRAILPCQDTPSVKLTYTAEVSVPKELVALMSAIRDGETPDPEDPSRKIYKFIQKVPIPCYLIALVVGALESRQIGPRTLVWSEKEQVEKSAYEFSETESMLKIAEDLGGPYVWGQYDLLVLPPSFPYGGMENPCLTFVTPTLLAGDKSLSNVIAHEISHSWTGNLVTNKTWDHFWLNEGHTVYLERHICGRLFGEKFRHFNALGGWGELQNSVKTFGETHPFTKLVVDLTDIDPDVAYSSVPYEKGFALLFYLEQLLGGPEIFLGFLKAYVEKFSYKSITTDDWKDFLYSYFKDKVDVLNQVDWNAWLYSPGLPPIKPNYDMTLTNACIALSQRWITAKEDDLNSFNATDLKDLSSHQLNEFLAQTLQRAPLPLGHIKRMQEVYNFNAINNSEIRFRWLRLCIQSKWEDAIPLALKMATEQGRMKFTRPLFKDLAAFDKSHDQAVRTYQEHKASMHPVTAMLVGKDLKVD 611
               SCOP domains d3chra2 A:1-208 Leukotriene A4 hydrolase N-terminal domain                                                                                                                                                      d3chra3 A:209-460 Leukotriene A4 hydrolase catalytic domain                                                                                                                                                                                                 d3chra1 A:461-610 Leukotriene A4 hydrolase C-terminal domain                                                                                           SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............eeeeeeeeeeeee....eeeeeeeeeeee....eeeeeeee..eeeeeeee..ee..eee...hhhhheeeeeeeeeee....eeeeeeeeee......eeeehhhhh......eeee.....hhhhh..........eeeeeeeeee...eeee..eeeeeee......eeeeeeeeeeeehhhhh.eeee..eeeeee..eeeeehhhhhhhhhhhh.hhhhhhhhhhhhhh.......eeee........ee....eeee.hhhh......hhhhhhhhhhh.....eee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh........hhhhhh.hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh.eeehhhhhhhhhhhhh..hhhhhh..hhhhhhhh..............hhhhhhhhhhhhhhhhhhh...hhhhhh..hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh...hhhhhhhhhhhhh.hhhhhhhhhhhhhhh..hhhhhhhhhhhhh...hhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------H------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ZINC_PROTE--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2  PDB: A:1-52 UniProt: 1-53 [INCOMPLETE]    Exon 1.3  PDB: A:53-96 UniProt: 54-97       ----------------------------------------Exon 1.5  PDB: A:137-15Exon 1.6  PDB: A:160-194           Exon 1.7          ------------------------Exon 1.10  PDB: A:237-283 UniProt: 238-284     1.11    Exon 1.12  PDB: A:292-31-------------------------------------Exon 1.14  PDB: A:353-401 UniProt: 354-402       ----------------------------------Exon 1.16  PDB: A:436-45------------------Exon 1.18  PDB: A:478-509       Exon 1.19  PDB: A:510-537   ----------------------------------Exon 1.21  PDB: A:572-610               Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------------------------------------------------Exon 1.4  PDB: A:96-136 UniProt: 97-137  ---------------------------------------------------------------------------Exon 1.9  PDB: A:212-236 ------------------------------------------------------------------------------Exon 1.13  PDB: A:315-352             ------------------------------------------------Exon 1.15  PDB: A:401-435          -----------------------Exon 1.17          -----------------------------------------------------------Exon 1.20  PDB: A:537-572           -------------------------------------- Transcript 1 (2)
                 3chr A   1 PEIVDTCSLASPASVCRTKHLHLRCSVDFTRRTLTGTAALTVQSQEDNLRSLVLDTKDLTIEKVVINGQEVKYALGERQSYKGSPMEISLPIALSKNQEIVIEISFETSPKSSALQWLTPEQTSGKEHPYLFSQCQAIHCRAILPCQDTPSVKLTYTAEVSVPKELVALMSAIRDGETPDPEDPSRKIYKFIQKVPIPCYLIALVVGALESRQIGPRTLVWSEKEQVEKSAYEFSETESMLKIAEDLGGPYVWGQYDLLVLPPSFPYGGMENPCLTFVTPTLLAGDKSLSNVIAHEISHSWTGNLVTNKTWDHFWLNEGHTVYLERHICGRLFGEKFRHFNALGGWGELQNSVKTFGETHPFTKLVVDLTDIDPDVAYSSVPYEKGFALLFYLEQLLGGPEIFLGFLKAYVEKFSYKSITTDDWKDFLYSYFKDKVDVLNQVDWNAWLYSPGLPPIKPNYDMTLTNACIALSQRWITAKEDDLNSFNATDLKDLSSHQLNEFLAQTLQRAPLPLGHIKRMQEVYNFNAINNSEIRFRWLRLCIQSKWEDAIPLALKMATEQGRMKFTRPLFKDLAAFDKSHDQAVRTYQEHKASMHPVTAMLVGKDLKVD 610
                                    10        20        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       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610

   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  (3, 3)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3CHR)

(-) Gene Ontology  (25, 25)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (LKHA4_HUMAN | P09960)
molecular function
    GO:0004177    aminopeptidase activity    Catalysis of the hydrolysis of N-terminal amino acid residues from in a polypeptide chain.
    GO:0004301    epoxide hydrolase activity    Catalysis of the reaction: an epoxide + H2O = a glycol.
    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:0004463    leukotriene-A4 hydrolase activity    Catalysis of the reaction: H(2)O + leukotriene A(4) = leukotriene B(4).
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0070006    metalloaminopeptidase activity    Catalysis of the hydrolysis of N-terminal amino acid residues from a polypeptide chain by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions.
    GO:0008237    metallopeptidase activity    Catalysis of the hydrolysis of peptide bonds by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions.
    GO:0008233    peptidase activity    Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
    GO:0042277    peptide binding    Interacting selectively and non-covalently with peptides, any of a group of organic compounds comprising two or more amino acids linked by peptide bonds.
    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:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0060509    Type I pneumocyte differentiation    The process in which a relatively unspecialized cell acquires specialized features of a Type I pneumocyte. A type I pneumocyte is a flattened cell with greatly attenuated cytoplasm and a paucity of organelles.
    GO:0006954    inflammatory response    The immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents. The process is characterized by local vasodilation, extravasation of plasma into intercellular spaces and accumulation of white blood cells and macrophages.
    GO:0019370    leukotriene biosynthetic process    The chemical reactions and pathways resulting in the formation of leukotriene, a pharmacologically active substance derived from a polyunsaturated fatty acid, such as arachidonic acid.
    GO:0006691    leukotriene metabolic process    The chemical reactions and pathways involving leukotriene, a pharmacologically active substance derived from a polyunsaturated fatty acid, such as arachidonic acid.
    GO:0043171    peptide catabolic process    The chemical reactions and pathways resulting in the breakdown of peptides, compounds of 2 or more (but usually less than 100) amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0043434    response to peptide hormone    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 peptide hormone stimulus. A peptide hormone is any of a class of peptides that are secreted into the blood stream and have endocrine functions in living animals.
    GO:0010043    response to zinc ion    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 zinc ion stimulus.
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:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    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.
    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
        LKHA4_HUMAN | P099601gw6 1h19 1hs6 1sqm 2r59 2vj8 3b7r 3b7s 3b7t 3b7u 3cho 3chp 3chq 3chs 3fh5 3fh7 3fh8 3fhe 3fts 3ftu 3ftv 3ftw 3ftx 3fty 3ftz 3fu0 3fu3 3fu5 3fu6 3fud 3fue 3fuf 3fuh 3fui 3fuj 3fuk 3ful 3fum 3fun 3u9w 4dpr 4l2l 4mkt 4ms6 4r7l 4rsy 4rvb 5aen 5bpp 5fwq 5n3w

(-) Related Entries Specified in the PDB File

1gw6 STRUCTURE OF LEUKOTRIENE A4 HYDROLASE D375N MUTANT
1h19 STRUCTURE OF LEUKOTRIENE A4 HYDROLASE E271Q MUTANT
1hs6 STRUCTURE OF LEUKOTRIENE A4 HYDROLASE COMPLEXED WITH BESTATIN
1sqm STRUCTURE OF LEUKOTRIENE A4 HYDROLASE R563A MUTANT
2vj8 STRUCTURE OF LEUKOTRIENE A4 HYDROLASE IN COMPLEX WITH HYDROXAMIC ACID BASED INHIBITOR
3cho STRUCTURE OF LEUKOTRIENE A4 HYDROLASE IN COMPLEX WITH 2- AMINO-N-[4-(PHENYLMETHOXY)PHENYL]-ACETAMIDE
3chp STRUCTURE OF LEUKOTRIENE A4 HYDROLASE IN COMPLEX WITH (3S)- 3-AMINO-4-OXO-4-[(4-PHENYLMETHOXYPHENYL)AMINO]BUTANOIC ACID
3chq STRUCTURE OF LEUKOTRIENE A4 HYDROLASE IN COMPLEX WITH N5- [4-(PHENYLMETHOXY)PHENYL]-L-GLUTAMINE
3chs STRUCTURE OF LEUKOTRIENE A4 HYDROLASE IN COMPLEX WITH (2S)- 2-AMINO-5-[[4-[(2S)-2-HYDROXY-2-PHENYL-ETHOXY]PHENYL]AMINO] -5-OXO-PENTANOIC ACID