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(-) Description

Title :  CLOSED CRYSTAL STRUCTURE OF CYCLOHEXANONE MONOOXYGENASE
 
Authors :  I. A. Mirza, B. J. Yachnin, A. M. Berghuis
Date :  31 Mar 09  (Deposition) - 05 May 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A
Keywords :  Flavoprotein Biocatalysis Baeyer-Villiger Oxidation Green Chemistry, Monooxygenase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  I. A. Mirza, B. J. Yachnin, S. Wang, S. Grosse, H. Bergeron, A. Imura, H. Iwaki, Y. Hasegawa, P. C. Lau, A. M. Berghuis
Crystal Structures Of Cyclohexanone Monooxygenase Reveal Complex Domain Movements And A Sliding Cofactor
J. Am. Chem. Soc. V. 131 8848 2009
PubMed-ID: 19385644  |  Reference-DOI: 10.1021/JA9010578

(-) Compounds

Molecule 1 - CYCLOHEXANONE MONOOXYGENASE
    ChainsA
    EC Number1.14.13.22
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    GeneCHNB, CHNB1
    Organism ScientificRHODOCOCCUS SP.
    Organism Taxid638919
    StrainHI-31

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
2NAP2Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:14 , GLY A:15 , GLY A:17 , PHE A:18 , GLY A:19 , ASP A:39 , LYS A:40 , GLY A:46 , THR A:47 , TRP A:48 , TRP A:50 , TYR A:53 , SER A:58 , ASP A:59 , THR A:60 , TYR A:65 , THR A:110 , GLU A:111 , VAL A:112 , ALA A:142 , VAL A:143 , GLY A:144 , ASN A:388 , ASN A:436 , LEU A:437 , NAP A:542 , NAP A:543 , HOH A:545 , HOH A:546 , HOH A:559 , HOH A:560 , HOH A:563 , HOH A:578BINDING SITE FOR RESIDUE FAD A 541
2AC2SOFTWARETYR A:53 , LEU A:57 , ASP A:59 , LEU A:146 , PRO A:152 , ILE A:184 , GLY A:185 , THR A:186 , GLY A:187 , SER A:188 , THR A:189 , GLN A:192 , ARG A:209 , THR A:210 , ARG A:329 , ILE A:350 , ALA A:379 , THR A:380 , GLY A:381 , PHE A:382 , TRP A:492 , FAD A:541 , HOH A:548 , HOH A:564 , HOH A:567 , HOH A:569 , HOH A:570 , HOH A:581 , HOH A:582 , HOH A:584 , HOH A:586 , HOH A:595BINDING SITE FOR RESIDUE NAP A 542
3AC3SOFTWARELYS A:40 , TRP A:50 , GLU A:111 , SER A:147 , ILE A:149 , ALA A:168 , ASN A:388 , FAD A:541 , HOH A:558 , HOH A:560 , HOH A:656BINDING SITE FOR RESIDUE NAP A 543

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3GWD)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3GWD)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3GWD)

(-) 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:531
 aligned with C0STX7_9NOCA | C0STX7 from UniProtKB/TrEMBL  Length:540

    Alignment length:531
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534 
         C0STX7_9NOCA     5 TTHTVDAVVIGAGFGGIYAVHKLHHELGLTTVGFDKADGPGGTWYWNRYPGALSDTESHLYRFSFDRDLLQESTWKTTYITQPEILEYLEDVVDRFDLRRHFKFGTEVTSALYLDDENLWEVTTDHGEVYRAKYVVNAVGLLSAINFPNLPGLDTFEGETIHTAAWPEGKSLAGRRVGVIGTGSTGQQVITSLAPEVEHLTVFVRTPQYSVPVGNRPVNPEQIAEIKADYDRIWERAKNSAVAFGFEESTLPAMSVSEEERNRIFQEAWDHGGGFRFMFGTFGDIATDEAANEAAASFIRAKVAEIIEDPETARKLMPKGLFAKRPLCDSGYYEVYNRPNVEAVAIKENPIREVTAKGVVTEDGVLHELDVLVFATGFDAVDGNYRRIEIRGRDGLHINDHWDGQPTSYLGVSTANFPNWFMVLGPNGPFTNLPPSIETQVEWISDTIGYAERNGVRAIEPTPEAEAEWTETCTEIANATLFTKGDSWIFGANIPGKKPSVLFYLGGLRNYRAVMAEVAADGYRGFEVKSA 535
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3gwdA01 A:5-152,A:383-535  [code=3.50.50.60, no name defined]                                                                                       --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------3gwdA01 A:5-152,A:383-535  [code=3.50.50.60, no name defined]                                                                                             CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeee..hhhhhhhhhhhhhh....eeee.......hhhhhh..................hhhhhhhh.......hhhhhhhhhhhhhhhh.hhh.ee....eeeeeee....eeeeee....eeeeeeeee..............hhhhh..eeee.hhh.........eeeee..hhhhhhhhhhhhhhh.eeeeee......ee......hhhhhhhhhhhhhhhhhhhhh.................hhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh.hhhhhhhhh..........ee..hhhhhhh..eeeee.....eeeee..eeee....eee..eeee.......hhhhhh.eeehhhhhhhhhhh.................eee.....ee..hhhhhhhhhhhhhhhhhhhhhhh...eeeehhhhhhhhhhhhhhhhhhhhhhhh.hhhhh...........ee..hhhhhhhhhhhhhhh....eeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3gwd A   5 TTHTVDAVVIGAGFGGIYAVHKLHHELGLTTVGFDKADGPGGTWYWNRYPGALSDTESHLYRFSFDRDLLQESTWKTTYITQPEILEYLEDVVDRFDLRRHFKFGTEVTSALYLDDENLWEVTTDHGEVYRAKYVVNAVGLLSAINFPNLPGLDTFEGETIHTAAWPEGKSLAGRRVGVIGTGSTGQQVITSLAPEVEHLTVFVRTPQYSVPVGNRPVNPEQIAEIKADYDRIWERAKNSAVAFGFEESTLPAMSVSEEERNRIFQEAWDHGGGFRFMFGTFGDIATDEAANEAAASFIRAKVAEIIEDPETARKLMPKGLFAKRPLCDSGYYEVYNRPNVEAVAIKENPIREVTAKGVVTEDGVLHELDVLVFATGFDAVDGNYRRIEIRGRDGLHINDHWDGQPTSYLGVSTANFPNWFMVLGPNGPFTNLPPSIETQVEWISDTIGYAERNGVRAIEPTPEAEAEWTETCTEIANATLFTKGDSWIFGANIPGKKPSVLFYLGGLRNYRAVMAEVAADGYRGFEVKSA 535
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534 

Chain A from PDB  Type:PROTEIN  Length:531
 aligned with Q6RXW1_9NOCA | Q6RXW1 from UniProtKB/TrEMBL  Length:540

    Alignment length:531
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534 
         Q6RXW1_9NOCA     5 TIHTVDAVVIGAGFGGIYAVHKLHHELGLTTVGFDKADGPGGTWYWNRYPGALSDTESHLYRFSFDRDLLQESTWKSTYITQPEILEYLEDVVDRFDLRRHFKFGTEVTSALYLDDENLWEVTTDHGEVYRAKYVVNAVGLLSAINFPNLPGLDTFEGETIHTAAWPEGKSLAGRRVGVIGTGSTGQQVITSLAPEVEHLTVFVRTPQYSVPVGNRPVTPEQIAEIKADYDRIWERAKNSAVAFGFEESTLPAMSVSEEERNRIFQEAWDHGGGFRFMFGTFGDIATDEAANEAAASFIRAKVAEIIEDPETARKLMPTGLFAKRPLCDSGYYEVYNRPNVEAVAIKENPIREVTAKGVVTEDGVLHELDVLVFATGFDAVDGNYRRIEIRGRDGLHINDHWDGQPTSYLGVSTANFPNWFMVLGPNGPFTNLPPSIETQVEWISDTIGYAERNGVRAIEPTPEAEAEWTETCTEIANATLFTKGDSWIFGANIPGKKPSVLFYLGGLRNYRAVMAEVAADGYRGFEVKSA 535
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3gwdA01 A:5-152,A:383-535  [code=3.50.50.60, no name defined]                                                                                       --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------3gwdA01 A:5-152,A:383-535  [code=3.50.50.60, no name defined]                                                                                             CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeee..hhhhhhhhhhhhhh....eeee.......hhhhhh..................hhhhhhhh.......hhhhhhhhhhhhhhhh.hhh.ee....eeeeeee....eeeeee....eeeeeeeee..............hhhhh..eeee.hhh.........eeeee..hhhhhhhhhhhhhhh.eeeeee......ee......hhhhhhhhhhhhhhhhhhhhh.................hhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh.hhhhhhhhh..........ee..hhhhhhh..eeeee.....eeeee..eeee....eee..eeee.......hhhhhh.eeehhhhhhhhhhh.................eee.....ee..hhhhhhhhhhhhhhhhhhhhhhh...eeeehhhhhhhhhhhhhhhhhhhhhhhh.hhhhh...........ee..hhhhhhhhhhhhhhh....eeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3gwd A   5 TTHTVDAVVIGAGFGGIYAVHKLHHELGLTTVGFDKADGPGGTWYWNRYPGALSDTESHLYRFSFDRDLLQESTWKTTYITQPEILEYLEDVVDRFDLRRHFKFGTEVTSALYLDDENLWEVTTDHGEVYRAKYVVNAVGLLSAINFPNLPGLDTFEGETIHTAAWPEGKSLAGRRVGVIGTGSTGQQVITSLAPEVEHLTVFVRTPQYSVPVGNRPVNPEQIAEIKADYDRIWERAKNSAVAFGFEESTLPAMSVSEEERNRIFQEAWDHGGGFRFMFGTFGDIATDEAANEAAASFIRAKVAEIIEDPETARKLMPKGLFAKRPLCDSGYYEVYNRPNVEAVAIKENPIREVTAKGVVTEDGVLHELDVLVFATGFDAVDGNYRRIEIRGRDGLHINDHWDGQPTSYLGVSTANFPNWFMVLGPNGPFTNLPPSIETQVEWISDTIGYAERNGVRAIEPTPEAEAEWTETCTEIANATLFTKGDSWIFGANIPGKKPSVLFYLGGLRNYRAVMAEVAADGYRGFEVKSA 535
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534 

   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 3GWD)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (7, 13)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q6RXW1_9NOCA | Q6RXW1)
molecular function
    GO:0004499    N,N-dimethylaniline monooxygenase activity    Catalysis of the reaction: N,N-dimethylaniline + NADPH + H+ + O2 = N,N-dimethylaniline N-oxide + NADP+ + H2O.
    GO:0050661    NADP binding    Interacting selectively and non-covalently with nicotinamide-adenine dinucleotide phosphate, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NADP+, or the reduced form, NADPH.
    GO:0050660    flavin adenine dinucleotide binding    Interacting selectively and non-covalently with FAD, flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes, in either the oxidized form, FAD, or the reduced form, FADH2.
    GO:0004497    monooxygenase activity    Catalysis of the incorporation of one atom from molecular oxygen into a compound and the reduction of the other atom of oxygen to water.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
biological process
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.

Chain A   (C0STX7_9NOCA | C0STX7)
molecular function
    GO:0004499    N,N-dimethylaniline monooxygenase activity    Catalysis of the reaction: N,N-dimethylaniline + NADPH + H+ + O2 = N,N-dimethylaniline N-oxide + NADP+ + H2O.
    GO:0050661    NADP binding    Interacting selectively and non-covalently with nicotinamide-adenine dinucleotide phosphate, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NADP+, or the reduced form, NADPH.
    GO:0050660    flavin adenine dinucleotide binding    Interacting selectively and non-covalently with FAD, flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes, in either the oxidized form, FAD, or the reduced form, FADH2.
    GO:0004497    monooxygenase activity    Catalysis of the incorporation of one atom from molecular oxygen into a compound and the reduction of the other atom of oxygen to water.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
biological process
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.

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 Related Entries

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

UniProtKB/Swiss-Prot
        Q6RXW1_9NOCA | Q6RXW13gwf
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        C0STX7_9NOCA | C0STX73gwf 3ucl 4rg3 4rg4

(-) Related Entries Specified in the PDB File

3gwf OPEN CRYSTAL STRUCTURE OF CYCLOHEXANONE MONOOXYGENASE