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(-) Description

Title :  HUMAN CYTOCHROME P450 2A6 IN COMPLEX WITH NICOTINE
 
Authors :  N. M. Devore, E. E. Scott
Date :  06 Apr 12  (Deposition) - 06 Jun 12  (Release) - 02 Jan 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Cytochrome P450 2A6, P450 2A6, Heme Protein, Monoxygenase, Drug Metabolism, Xenobiotic Metabolism, Endoplasmic Reticulum, Membrane, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. M. Devore, E. E. Scott
Nicotine And 4-(Methylnitrosamino)-1-(3-Pyridyl)-1-Butanone Binding And Access Channel In Human Cytochrome P450 2A6 And 2A13 Enzymes.
J. Biol. Chem. V. 287 26576 2012
PubMed-ID: 22700965  |  Reference-DOI: 10.1074/JBC.M112.372813

(-) Compounds

Molecule 1 - CYTOCHROME P450 2A6
    Chains: A, B, C, D
    EC Number: 1.14.14.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PKK2A6DH
    Expression System Strain: TOPP3
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 30-494
    Gene: CYP2A3, CYP2A6
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: CYPIIA6, COUMARIN 7-HYDROXYLASE, CYTOCHROME P450 IIA3, CYTOCHROME P450(I)

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric Unit (2, 8)
No.NameCountTypeFull Name
1HEM4Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
2NCT4Ligand/Ion(S)-3-(1-METHYLPYRROLIDIN-2-YL)PYRIDINE
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
2NCT1Ligand/Ion(S)-3-(1-METHYLPYRROLIDIN-2-YL)PYRIDINE
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
2NCT1Ligand/Ion(S)-3-(1-METHYLPYRROLIDIN-2-YL)PYRIDINE
Biological Unit 3 (2, 2)
No.NameCountTypeFull Name
1HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
2NCT1Ligand/Ion(S)-3-(1-METHYLPYRROLIDIN-2-YL)PYRIDINE
Biological Unit 4 (2, 2)
No.NameCountTypeFull Name
1HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
2NCT1Ligand/Ion(S)-3-(1-METHYLPYRROLIDIN-2-YL)PYRIDINE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:101 , VAL A:117 , ARG A:128 , GLY A:301 , GLY A:302 , THR A:305 , ARG A:372 , LEU A:395 , PRO A:431 , PHE A:432 , SER A:433 , ARG A:437 , ASN A:438 , CYS A:439 , PHE A:440 , GLY A:441 , NCT A:501 , HOH A:647BINDING SITE FOR RESIDUE HEM A 500
2AC2SOFTWAREPHE A:107 , PHE A:209 , ASN A:297 , GLY A:301 , THR A:305 , PHE A:480 , HEM A:500BINDING SITE FOR RESIDUE NCT A 501
3AC3SOFTWAREARG B:101 , VAL B:117 , ARG B:128 , GLY B:301 , GLY B:302 , THR B:305 , GLN B:360 , SER B:369 , ARG B:372 , LEU B:395 , PRO B:431 , PHE B:432 , SER B:433 , ILE B:434 , ARG B:437 , ASN B:438 , CYS B:439 , PHE B:440 , NCT B:501BINDING SITE FOR RESIDUE HEM B 500
4AC4SOFTWAREPHE B:107 , ASN B:297 , THR B:305 , HEM B:500BINDING SITE FOR RESIDUE NCT B 501
5AC5SOFTWAREARG C:101 , VAL C:117 , ARG C:128 , GLY C:301 , GLY C:302 , THR C:305 , VAL C:306 , THR C:309 , LEU C:370 , ARG C:372 , LEU C:395 , PRO C:431 , PHE C:432 , SER C:433 , ARG C:437 , ASN C:438 , CYS C:439 , PHE C:440 , NCT C:501BINDING SITE FOR RESIDUE HEM C 500
6AC6SOFTWAREPHE C:107 , PHE C:209 , ASN C:297 , GLY C:301 , HEM C:500BINDING SITE FOR RESIDUE NCT C 501
7AC7SOFTWAREGLY D:301 , THR D:305 , LEU D:370 , PHE D:480 , HEM D:502BINDING SITE FOR RESIDUE NCT D 501
8AC8SOFTWAREARG D:101 , VAL D:117 , ARG D:128 , GLY D:301 , GLY D:302 , THR D:305 , VAL D:306 , SER D:369 , LEU D:370 , ARG D:372 , LEU D:395 , PRO D:431 , PHE D:432 , SER D:433 , ARG D:437 , CYS D:439 , PHE D:440 , GLY D:441 , ALA D:445 , NCT D:501 , HOH D:618BINDING SITE FOR RESIDUE HEM D 502

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4EJJ)

(-) 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:465
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains d4ejja_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............hhhhh...hhhhhhhhhhhhhh.eeeeee..eeeeeehhhhhhhhhhh.......ee..hhhhhhhhh.......hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhh.......ee....eee..eee....eeeehhhhhhh...........hhhhhh.......................hhhhhhhhhhhhhhhhhhheeeee..hhhhh...eeee...eee....eeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ejj A  30 KGKLPPGPTPLPFIGNYLQLNTEQMYNSLMKISERYGPVFTIHLGPRRVVVLCGHDAVREALVDQAEEFSGRGEQATFDWVFKGYGVVFSNGERAKQLRRFSIATLRDFGVGKRGIEERIQEEAGFLIDALRGTGGANIDPTFFLSRTVSNVISSIVFGDRFDYKDKEFLSLLRMMLGIFQFTSTSTGQLYEMFSSVMKHLPGPQQQAFQLLQGLEDFIAKKVEHNQRTLDPNSPRDFIDSFLIRMQEEEKNPNTEFYLKNLVMTTLNLFIGGTETVSTTLRYGFLLLMKHPEVEAKVHEEIDRVIGKNRQPKFEDRAKMPYMEAVIHEIQRFGDVIPMSLARRVKKDTKFRDFFLPKGTEVYPMLGSVLRDPSFFSNPQDFNPQHFLNEKGQFKKSDAFVPFSIGKRNCFGEGLARMELFLFFTTVMQNFRLKSSQSPKDIDVSPKHVGFATIPRNYTMSFLPR 494
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489     


Chain B from PDB  Type:PROTEIN  Length:464
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains d4ejjb_ B: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............hhhhh...hhhhhhhhhhhhhh.eeeeee..eeeeeehhhhhhhhhhh.......ee..hhhhhhhhh.......hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhh.......ee....eee..eee....eeeehhhhhhh...........hhhhhh.......................hhhhhhhhhhhhhhhhhhhheeee..........eeee...eee....eeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ejj B  31 GKLPPGPTPLPFIGNYLQLNTEQMYNSLMKISERYGPVFTIHLGPRRVVVLCGHDAVREALVDQAEEFSGRGEQATFDWVFKGYGVVFSNGERAKQLRRFSIATLRDFGVGKRGIEERIQEEAGFLIDALRGTGGANIDPTFFLSRTVSNVISSIVFGDRFDYKDKEFLSLLRMMLGIFQFTSTSTGQLYEMFSSVMKHLPGPQQQAFQLLQGLEDFIAKKVEHNQRTLDPNSPRDFIDSFLIRMQEEEKNPNTEFYLKNLVMTTLNLFIGGTETVSTTLRYGFLLLMKHPEVEAKVHEEIDRVIGKNRQPKFEDRAKMPYMEAVIHEIQRFGDVIPMSLARRVKKDTKFRDFFLPKGTEVYPMLGSVLRDPSFFSNPQDFNPQHFLNEKGQFKKSDAFVPFSIGKRNCFGEGLARMELFLFFTTVMQNFRLKSSQSPKDIDVSPKHVGFATIPRNYTMSFLPR 494
                                    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    


Chain C from PDB  Type:PROTEIN  Length:464
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains d4ejjc_ C: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............hhhhhhhhhhhhhhhhhhhhhh.eeeeee..eeeeee.hhhhhhhhhh.......ee..hhhhhhhhh.......hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh.......ee....eee..eee....eeeehhhhhh............hhhhhh.......................hhhhhhhhhhhhhhhhhhheeeee..hhhhh...eeee...eee....eeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ejj C  31 GKLPPGPTPLPFIGNYLQLNTEQMYNSLMKISERYGPVFTIHLGPRRVVVLCGHDAVREALVDQAEEFSGRGEQATFDWVFKGYGVVFSNGERAKQLRRFSIATLRDFGVGKRGIEERIQEEAGFLIDALRGTGGANIDPTFFLSRTVSNVISSIVFGDRFDYKDKEFLSLLRMMLGIFQFTSTSTGQLYEMFSSVMKHLPGPQQQAFQLLQGLEDFIAKKVEHNQRTLDPNSPRDFIDSFLIRMQEEEKNPNTEFYLKNLVMTTLNLFIGGTETVSTTLRYGFLLLMKHPEVEAKVHEEIDRVIGKNRQPKFEDRAKMPYMEAVIHEIQRFGDVIPMSLARRVKKDTKFRDFFLPKGTEVYPMLGSVLRDPSFFSNPQDFNPQHFLNEKGQFKKSDAFVPFSIGKRNCFGEGLARMELFLFFTTVMQNFRLKSSQSPKDIDVSPKHVGFATIPRNYTMSFLPR 494
                                    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    


Chain D from PDB  Type:PROTEIN  Length:464
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains d4ejjd_ D: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............hhhhhhhhhhhhhhhhhhhhhh.eeeeee..eeeeee.hhhhhhhhhh.......ee..hhhhhhhhh.......hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh......hhhhhh.hhhhhhhhhhhhhhhh.......ee....eee..eee....eeeehhhhhhh...........hhhhhh.......................hhhhhhhhhhhhhhhhhhhheeee..hhhhh...eeee...eee....eeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ejj D  31 GKLPPGPTPLPFIGNYLQLNTEQMYNSLMKISERYGPVFTIHLGPRRVVVLCGHDAVREALVDQAEEFSGRGEQATFDWVFKGYGVVFSNGERAKQLRRFSIATLRDFGVGKRGIEERIQEEAGFLIDALRGTGGANIDPTFFLSRTVSNVISSIVFGDRFDYKDKEFLSLLRMMLGIFQFTSTSTGQLYEMFSSVMKHLPGPQQQAFQLLQGLEDFIAKKVEHNQRTLDPNSPRDFIDSFLIRMQEEEKNPNTEFYLKNLVMTTLNLFIGGTETVSTTLRYGFLLLMKHPEVEAKVHEEIDRVIGKNRQPKFEDRAKMPYMEAVIHEIQRFGDVIPMSLARRVKKDTKFRDFFLPKGTEVYPMLGSVLRDPSFFSNPQDFNPQHFLNEKGQFKKSDAFVPFSIGKRNCFGEGLARMELFLFFTTVMQNFRLKSSQSPKDIDVSPKHVGFATIPRNYTMSFLPR 494
                                    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
   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, 4)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (24, 24)

Asymmetric Unit(hide GO term definitions)

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  4ejj
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  CP2A6_HUMAN | P11509
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 Related Entries

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

UniProtKB/Swiss-Prot
        CP2A6_HUMAN | P11509: 1z10 1z11 2fdu 2fdv 2fdw 2fdy 2pg5 2pg6 2pg7 3ebs 3t3q 3t3r 4rui

(-) Related Entries Specified in the PDB File

1z10 CRYSTAL STRUCTURE OF HUMAN MICROSOMAL P450 2A6 WITH COUMARIN BOUND
1z11 CRYSTAL STRUCTURE OF HUMAN MICROSOMAL P450 2A6 WITH METHOXSALEN BOUND
2fdu MICROSOMAL P450 2A6 WITH THE INHIBITOR N,N-DIMETHYL(5- (OYRIDIN-3-YL)FURAN-2-YL)METHANAMINE BOUND
2fdv MICROSOMAL P450 2A6 WITH THE INHIBITOR N-METHYL(5-(PYRIDIN- 3-YL)FURAN-2-YL)METHANAMINE BOUND
2fdw CRYSTAL STRUCTURE OF HUMAN MICROSOMAL P450 2A6 WITH THE INHIBITOR (5-(PYRIDIN-3-YL)FURAN-2-YL)METHANAMINE BOUND
2fdy MICROSOMAL P450 2A6 WITH THE INHIBITOR ADRITHIOL BOUND
2pg5 CRYSTAL STRUCTURE OF HUMAN MICROSOMAL P450 2A6 N297Q
2pg6 CRYSTAL STRUCTURE OF HUMAN MICROSOMAL P450 2A6 L240C/N297Q
2pg7 CRYSTAL STRUCTURE OF HUMAN MICROSOMAL P450 2A6 N297Q/I300V
3ebs HUMAN CYTOCHROME P450 2A6 I208S/I300F/G301A/S369G IN COMPLEX WITH PHENACETIN
3t3r HUMAN CYTOCHROME P450 2A6 IN COMPLEX WITH PILOCARPINE
4ejg
4ejh
4eji