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(-) Description

Title :  CRYSTAL STRUCTURE OF ORYZA SATIVA FATTY ACID ALPHA-DIOXYGENASE
 
Authors :  G. Zhu, M. Koszelak-Rosenblum, M. G. Malkowski
Date :  22 May 13  (Deposition) - 21 Aug 13  (Release) - 16 Oct 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.98
Chains :  Asym./Biol. Unit :  A
Keywords :  Piox, Cox-Like Protein, Fatty Acid Alpha-Dioxygenase, Heme Binding, Calcium Binding, Monotopic Membrane Protein, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Zhu, M. Koszelak-Rosenblum, M. G. Malkowski
Crystal Structures Of Alpha-Dioxygenase From Oryza Sativa: Insights Into Substrate Binding And Activation By Hydrogen Peroxide.
Protein Sci. V. 22 1432 2013
PubMed-ID: 23934749  |  Reference-DOI: 10.1002/PRO.2327

(-) Compounds

Molecule 1 - FATTY ACID ALPHA-OXIDASE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Common: RED RICE
    Organism Scientific: ORYZA SATIVA
    Organism Taxid: 4530

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (9, 18)

Asymmetric/Biological Unit (9, 18)
No.NameCountTypeFull Name
11PE1Ligand/IonPENTAETHYLENE GLYCOL
2CA1Ligand/IonCALCIUM ION
3CL4Ligand/IonCHLORIDE ION
4DMU1Ligand/IonDECYL-BETA-D-MALTOPYRANOSIDE
5HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
6NA2Ligand/IonSODIUM ION
7PEG4Ligand/IonDI(HYDROXYETHYL)ETHER
8PG43Ligand/IonTETRAETHYLENE GLYCOL
9PGE1Ligand/IonTRIETHYLENE GLYCOL

(-) Sites  (18, 18)

Asymmetric Unit (18, 18)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREALA A:149 , ILE A:152 , GLN A:153 , VAL A:156 , HIS A:157 , ASP A:161 , HIS A:162 , ASN A:260 , TRP A:262 , THR A:376 , TYR A:379 , MET A:381 , HIS A:382 , ILE A:416 , PHE A:453 , LEU A:472 , LEU A:475 , ARG A:479 , ARG A:483 , HOH A:815 , HOH A:843 , HOH A:996 , HOH A:1180BINDING SITE FOR RESIDUE HEM A 701
02AC2SOFTWARESER A:19 , LYS A:20 , MET A:21 , SER A:22 , PHE A:23 , LYS A:26 , PHE A:31 , ARG A:38 , ILE A:348 , PG4 A:709 , HOH A:829 , HOH A:928 , HOH A:1055BINDING SITE FOR RESIDUE DMU A 702
03AC3SOFTWAREASN A:54 , ARG A:57BINDING SITE FOR RESIDUE PG4 A 703
04AC4SOFTWAREPHE A:24BINDING SITE FOR RESIDUE PEG A 704
05AC5SOFTWAREASN A:39 , HIS A:42 , LYS A:43 , ARG A:492 , ILE A:498 , PRO A:499 , ILE A:500 , ASP A:505 , GLU A:536 , NA A:717 , HOH A:832 , HOH A:1029 , HOH A:1117BINDING SITE FOR RESIDUE 1PE A 705
06AC6SOFTWAREGLU A:490 , ARG A:493 , ARG A:494 , PHE A:496BINDING SITE FOR RESIDUE PGE A 706
07AC7SOFTWAREARG A:590 , LYS A:606 , SER A:608 , TYR A:618 , NA A:718BINDING SITE FOR RESIDUE PG4 A 707
08AC8SOFTWAREILE A:239 , GLY A:240 , ASP A:241 , GLY A:243 , LYS A:274BINDING SITE FOR RESIDUE PEG A 708
09AC9SOFTWAREALA A:34 , PHE A:35 , ARG A:38 , DMU A:702 , HOH A:1119BINDING SITE FOR RESIDUE PG4 A 709
10BC1SOFTWARELYS A:323 , ARG A:326 , HOH A:1023 , HOH A:1028BINDING SITE FOR RESIDUE PEG A 710
11BC2SOFTWAREARG A:517 , ALA A:518 , ILE A:519BINDING SITE FOR RESIDUE PEG A 711
12BC3SOFTWARETHR A:210 , TRP A:212 , ASP A:214 , SER A:216 , HOH A:874 , HOH A:1085BINDING SITE FOR RESIDUE CA A 712
13BC4SOFTWARELYS A:309 , TRP A:333 , HOH A:1132BINDING SITE FOR RESIDUE CL A 713
14BC5SOFTWAREARG A:330 , LYS A:339 , HOH A:954BINDING SITE FOR RESIDUE CL A 714
15BC6SOFTWAREGLY A:350 , ILE A:352 , LEU A:353 , HOH A:922BINDING SITE FOR RESIDUE CL A 715
16BC7SOFTWAREHIS A:311 , TYR A:379BINDING SITE FOR RESIDUE CL A 716
17BC8SOFTWAREASP A:505 , 1PE A:705 , HOH A:980 , HOH A:981 , HOH A:1117BINDING SITE FOR RESIDUE NA A 717
18BC9SOFTWARESER A:608 , PG4 A:707 , HOH A:1228BINDING SITE FOR RESIDUE NA A 718

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4KVK)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Ser A:121 -Pro A:122

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4KVK)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4KVK)

(-) Exons   (0, 0)

(no "Exon" information available for 4KVK)

(-) 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:611
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.............hhhhh.....................ee.................hhhhhhhhhh............hhhhhhhhhhhhhhhh........eeee.hhhhhh.....eeee.....ee.......ee.ee.......hhhhhh.........................................hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh..hhhhhhhhh.........................hhhhhhhhhhhhhh..eeeee.............eeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhh..............hhhhhhhhhhhhh...hhhhhhhhh......hhhhh..hhhhhhhhhhhhh......hhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh............. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kvk A   8 GSVHPDLRDVFSKMSFFDKIGFLFIHAFDKRNLWHKVPVPIGLLYLNTRRTLLEKYNLLAVGRSSHGALFDPKEFLYRTEDGKYNDPHNAEAGSQNTFFGRNMEPVDQQDELMSPDPFVVATKLLARREYKDTGKQFNILAAAWIQFMVHDWMDHMEDTGQIGITAPKEVANECPLKSFKFHPTKELPTNSDGIKIGHYNIRTAWWDGSAVYGNNEERAEKLRTYVDGKLVIGDDGLLLHKENGVALSGDIRNSWAGVSILQALFVKEHNAVCDAIKEEHPNLSDEELYRYAKLVTSAVIAKVHTIDWTVELLKTKTMRAAMRANWYGLLGKKIKDTFGHIGGPILGGLVGLKKPNNHGVPYSLTEEFTSVYRMHSLIPSTLKLRDPTGQPDANNSPPCLEDIDIGEMIGLKGEEQLSKIGFEKQALSMGYQACGALELWNYPSFFRNLIPQNLDGTNRSDRIDLAALEVYRDRERSVPRYNEFRRRLFLIPIKSWEDLTSDKDAIETIRAIYGDDVEKLDLLVGLMAEKKIKGFAISETAFNIFILMASRRLEADRFFTSNFNEETYTKKGMQWVKTTEGLRDVINRHYPEITAKWMKSSSAFSVWDADY 618
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       547       557       567       577       587       597       607       617
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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 4KVK)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4KVK)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4KVK)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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        Q9M5J1_ORYSA | Q9M5J1: 4kvj 4kvl

(-) Related Entries Specified in the PDB File

4kvj 4kvl