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(-) Description

Title :  STRUCTURE OF THE A82F BM3 HEME DOMAIN IN COMPLEX WITH OMEPRAZOLE
 
Authors :  D. Leys
Date :  26 Apr 13  (Deposition) - 10 Jul 13  (Release) - 02 Oct 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.89
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  P450, Monooxygenase, Oxidoreductase-Oxidoreductase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. F. Butler, C. Peet, A. E. Mason, M. W. Voice, D. Leys, A. W. Munro
Key Mutations Alter The Cytochrome P450 Bm3 Conformational Landscape And Remove Inherent Substrate Bias.
J. Biol. Chem. V. 288 25387 2013
PubMed-ID: 23828198  |  Reference-DOI: 10.1074/JBC.M113.479717

(-) Compounds

Molecule 1 - BIFUNCTIONAL P-450/NADPH-P450 REDUCTASE
    Chains: A, B
    EC Number: 1.14.14.1, 1.6.2.4
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: P450 BM3 HEME DOMAIN
    Gene: CYP102A1, CYP102
    Mutation: YES
    Organism Scientific: BACILLUS MEGATERIUM
    Organism Taxid: 1404
    Synonym: CYTOCHROME P450(BM-3), CYTOCHROME P450BM-3, CYTOCHROME P450 102, NADPH--CYTOCHROME P450 REDUCTASE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
11C62Ligand/Ion6-METHOXY-2-{[(4-METHOXY-3,5-DIMETHYLPYRIDIN-2-YL)METHYL]SULFANYL}-1H-BENZIMIDAZOLE
2HEM2Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
11C61Ligand/Ion6-METHOXY-2-{[(4-METHOXY-3,5-DIMETHYLPYRIDIN-2-YL)METHYL]SULFANYL}-1H-BENZIMIDAZOLE
2HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
11C61Ligand/Ion6-METHOXY-2-{[(4-METHOXY-3,5-DIMETHYLPYRIDIN-2-YL)METHYL]SULFANYL}-1H-BENZIMIDAZOLE
2HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:69 , LEU A:86 , PHE A:87 , TRP A:96 , PHE A:107 , ALA A:264 , GLY A:265 , THR A:268 , THR A:269 , THR A:327 , PHE A:331 , PRO A:392 , PHE A:393 , GLY A:394 , ARG A:398 , ALA A:399 , CYS A:400 , ILE A:401 , GLY A:402 , ALA A:406 , HOH A:623 , HOH A:625 , HOH A:678 , HOH A:714 , HOH A:788 , HOH A:948BINDING SITE FOR RESIDUE HEM A 501
2AC2SOFTWAREVAL A:26 , TYR A:51 , ALA A:74 , PHE A:87 , LEU A:188 , ALA A:264 , ALA A:328 , PRO A:329 , ALA A:330 , LEU A:437 , HOH A:756 , HOH A:761 , HOH A:781BINDING SITE FOR RESIDUE 1C6 A 502
3AC3SOFTWARELYS B:69 , LEU B:75 , LEU B:86 , PHE B:87 , TRP B:96 , PHE B:107 , PHE B:261 , ALA B:264 , GLY B:265 , THR B:268 , THR B:269 , THR B:327 , PHE B:331 , PRO B:392 , PHE B:393 , GLY B:394 , ARG B:398 , ALA B:399 , CYS B:400 , ILE B:401 , GLY B:402 , HOH B:621 , HOH B:624 , HOH B:653 , HOH B:725 , HOH B:785 , HOH B:859BINDING SITE FOR RESIDUE HEM B 501
4AC4SOFTWAREVAL B:26 , PHE B:87 , LEU B:188 , ALA B:264 , ALA B:328 , PRO B:329 , ALA B:330 , LEU B:437 , HOH B:654 , HOH B:798 , HOH B:861BINDING SITE FOR RESIDUE 1C6 B 502

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4KEW)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4KEW)

(-) 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:450
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains d4kewa_ A: Cytochrome P450 bm-3                                                                                                                                                                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........hhhhhhhhhhh..hhhhhhhhhhhhhh.eeeeee..eeeeee.hhhhhhhhh....eeee.hhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eehhhhhhhhhhhhhhhhhhh...hhhhh...hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh....eeeeee...eee...eee....eeeeehhhhh.hhhhhh......hhhhhhhhhhh.........hhhhh..hhhhhhhhhhhhhhhhhhheeee........eee...eee...eeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4kew A   3 KEMPQPKTFGELKNLPLLNTDKPVQALMKIADELGEIFKFEAPGRVTRYLSSQRLIKEACDESRFDKNLSQALKFVRDFFGDGLFTSWTHEKNWKKAHNILLPSFSQQAMKGYHAMMVDIAVQLVQKWERLNADEHIEVPEDMTRLTLDTIGLCGFNYRFNSFYRDQPHPFITSMVRALDEAMNKLQRANPDDPAYDENKRQFQEDIKVMNDLVDKIIADRKASSDDLLTHMLNGKDPETGEPLDDENIRYQIITFLIAGHETTSGLLSFALYFLVKNPHVLQKAAEEAARVLVDPVPSYKQVKQLKYVGMVLNEALRLWPTAPAFSLYAKEDTVLGGEYPLEKGDELMVLIPQLHRDKTIWGDDVEEFRPERFENPSAIPQHAFKPFGNGQRACIGQQFALHEATLVLGMMLKHFDFEDHTNYELDIKETLTLKPEGFVVKAKSKKIPL 455
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222   ||  235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455
                                                                                                                                                                                                                                                         226|                                                                                                                                                                                                                                 
                                                                                                                                                                                                                                                          230                                                                                                                                                                                                                                 


Chain B from PDB  Type:PROTEIN  Length:443
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains d4kewb_ B: Cytochrome P450 bm-3                                                                                                                                                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhh..hhhhhhhhhhhhhh.eeeeee..eeeeee.hhhhhhhhh....eeee.hhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eehhhhhhhhhhhhhhhhhhh...hhhhh...hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh....eeeeee...eee...eee....eeeeehhhhh.hhhhhh......hhhhhhhhhhh.........hhhhh..hhhhhhhhhhhhhhhhhhheeee........eee...eee...eeeeee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kew B   3 KEMPQPLKNLPLLNTDKPVQALMKIADELGEIFKFEAPGRVTRYLSSQRLIKEACDESRFDKNLSQALKFVRDFFGDGLFTSWTHEKNWKKAHNILLPSFSQQAMKGYHAMMVDIAVQLVQKWERLNADEHIEVPEDMTRLTLDTIGLCGFNYRFNSFYRDQPHPFITSMVRALDEAMNKLQRANPDDPAYDENKRQFQEDIKVMNDLVDKIIADRKSDDLLTHMLNGKDPETGEPLDDENIRYQIITFLIAGHETTSGLLSFALYFLVKNPHVLQKAAEEAARVLVDPVPSYKQVKQLKYVGMVLNEALRLWPTAPAFSLYAKEDTVLGGEYPLEKGDELMVLIPQLHRDKTIWGDDVEEFRPERFENPSAIPQHAFKPFGNGQRACIGQQFALHEATLVLGMMLKHFDFEDHTNYELDIKETLTLKPEGFVVKAKSKKIPL 455
                                 || 17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217      |232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452   
                                 8|                                                                                                                                                                                                               224|                                                                                                                                                                                                                                 
                                 14                                                                                                                                                                                                                230
   Legend:   → Mismatch (orange background)
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  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  (1, 2)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (15, 15)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        CPXB_BACMB | P14779: 1bu7 1bvy 1fag 1fah 1jme 1jpz 1p0v 1p0w 1p0x 1smi 1smj 1yqo 1yqp 1zo4 1zo9 1zoa 2bmh 2hpd 2ij2 2ij3 2ij4 2j1m 2j4s 2nnb 2uwh 2x7y 2x80 3ben 3cbd 3dgi 3ekb 3ekd 3ekf 3hf2 3kx3 3kx4 3kx5 3m4v 3npl 3psx 3wsp 4dqk 4dql 4dtw 4dty 4dtz 4du2 4dua 4dub 4duc 4dud 4due 4duf 4h23 4h24 4hgf 4hgg 4hgh 4hgi 4hgj 4key 4kf0 4kf2 4kpa 4kpb 4o4p 4rsn 4wg2 4zf6 4zf8 4zfa 4zfb 5b2u 5b2v 5b2w 5b2x 5b2y 5dyp 5dyz 5e78 5e7y 5e9z 5jq2 5jqu 5jqv 5jtd

(-) Related Entries Specified in the PDB File

4key 4kf0 4kf2