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(-) Description

Title :  CRYSTAL STRUCTURE OF THE MIDAZOLAM-BOUND HUMAN CYP3A4
 
Authors :  I. Sevrioukova, T. Poulos
Date :  20 Sep 16  (Deposition) - 07 Dec 16  (Release) - 25 Jan 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A (1x),B (1x),C (1x)
Keywords :  Cytochrome P450, Cyp3A4, Monooxygenase, Drug Metabolism, Midazolam, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  I. F. Sevrioukova, T. L. Poulos
Structural Basis For Regiospecific Midazolam Oxidation By Human Cytochrome P450 3A4.
Proc. Natl. Acad. Sci. V. 114 486 2017 U. S. A.
PubMed-ID: 28031486  |  Reference-DOI: 10.1073/PNAS.1616198114

(-) Compounds

Molecule 1 - CYTOCHROME P450 3A4
    Chains: A, B, C
    EC Number: 1.14.13.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PCWORI
    Gene: CYP3A4, CYP3A3
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: HUMAN CYP3A4 WITH RESIDUES 3-22 DELETED AND THE ADDITION C-TERMINAL 4-HISTIDINE TAG
    Synonym: 1,8-CINEOLE 2-EXO-MONOOXYGENASE,ALBENDAZOLE MONOOXYGENASE, ALBENDAZOLE SULFOXIDASE,CYPIIIA3,CYPIIIA4,CHOLESTEROL 25-HYDROXYLASE, CYTOCHROME P450 3A3,CYTOCHROME P450 HLP,CYTOCHROME P450 NF-25, CYTOCHROME P450-PCN1,NIFEDIPINE OXIDASE,QUININE 3-MONOOXYGENASE, TAUROCHENODEOXYCHOLATE 6-ALPHA-HYDROXYLASE

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): A (1x)B (1x)C (1x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric Unit (2, 6)
No.NameCountTypeFull Name
108J3Ligand/Ion8-CHLORO-6-(2-FLUOROPHENYL)-1-METHYL-4H-IMIDAZO[1,5-A][1,4]BENZODIAZEPINE
2HEM3Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
108J1Ligand/Ion8-CHLORO-6-(2-FLUOROPHENYL)-1-METHYL-4H-IMIDAZO[1,5-A][1,4]BENZODIAZEPINE
2HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:105 , ILE A:118 , SER A:119 , TRP A:126 , ARG A:130 , PHE A:302 , ALA A:305 , THR A:309 , ALA A:370 , LEU A:373 , ARG A:375 , PRO A:434 , PHE A:435 , GLY A:436 , SER A:437 , ARG A:440 , ASN A:441 , CYS A:442 , ILE A:443 , PHE A:447 , ALA A:448 , MET A:452 , 08J A:602binding site for residue HEM A 601
2AC2SOFTWAREARG A:105 , SER A:119 , LEU A:216 , ALA A:305 , THR A:309 , GLY A:481 , HEM A:601binding site for residue 08J A 602
3AC3SOFTWAREARG B:105 , ILE B:118 , TRP B:126 , ARG B:130 , PHE B:302 , ALA B:305 , THR B:309 , THR B:310 , ALA B:370 , LEU B:373 , ARG B:375 , PRO B:434 , PHE B:435 , GLY B:436 , ARG B:440 , ASN B:441 , CYS B:442 , ILE B:443 , ALA B:448 , 08J B:602 , HOH B:706binding site for residue HEM B 601
4AC4SOFTWAREARG B:105 , SER B:119 , LEU B:216 , ALA B:305 , THR B:309 , ALA B:370 , LEU B:482 , HEM B:601binding site for residue 08J B 602
5AC5SOFTWAREARG C:105 , ILE C:118 , SER C:119 , TRP C:126 , ARG C:130 , PHE C:302 , ALA C:305 , THR C:309 , VAL C:313 , ILE C:369 , ARG C:375 , PRO C:434 , PHE C:435 , ARG C:440 , ASN C:441 , CYS C:442 , ILE C:443 , ALA C:448 , 08J C:602binding site for residue HEM C 601
6AC6SOFTWAREARG C:105 , SER C:119 , LEU C:216 , THR C:309 , ILE C:369 , HEM C:601binding site for residue 08J C 602

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5TE8)

(-) Cis Peptide Bonds  (5, 5)

Asymmetric Unit
No.Residues
1Ile A:473 -Pro A:474
2His B:287 -Lys B:288
3Ile B:473 -Pro B:474
4Pro C:340 -Asn C:341
5Ile C:473 -Pro C:474

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5TE8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5TE8)

(-) Exons   (0, 0)

(no "Exon" information available for 5TE8)

(-) 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:470
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhh...hhhhhhh...........hhhhhhhhhhhhhhhhhhhhh.eeeeee..eeeeee.hhhhhhhhhh...............hhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eehhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhh................hhhhhhhhh.........hhhhhhhhhhhhhhhh.......hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhh.....eeee....eee..eee....eeeehhhhhhh...........hhhhhh.......................hhhhhhhhhhhhhhhhhhheeee.......................eeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5te8 A   2 AYLYGTHSHGLFKKLGIPGPTPLPFLGNILSYHKGFCMFDMECHKKYGKVWGFYDGQQPVLAITDPDMIKTVLVKECYSVFTNRRPFGPVGFMKSAISIAEDEEWKRLRSLLSPTFTSGKLKEMVPIIAQYGDVLVRNLRREAETGKPVTLKDVFGAYSMDVITSTSFGVNIDSLNNPQDPFVENTKKLLRFDFLDPFFLSITVFPFLIPILEVLNICVFPREVTNFLRKSVKRMKESRLDTQKHRVDFLQLMIDSQNSHKALSDLELVAQSIIFIFAGYETTSSVLSFIMYELATHPDVQQKLQEEIDAVLPNKAPPTYDTVLQMEYLDMVVNETLRLFPIAMRLERVCKKDVEINGMFIPKGVVVMIPSYALHRDPKYWTEPEKFLPERFSKKNKDNIDPYIYTPFGSGPRNCIGMRFALMNMKLALIRVLQNFSFKPCKETQIPLKLSLGGLLQPEKPVVLKVESRD 497
                            ||      31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261|      272       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497
                            ||                                                                                                                                                                                                                                           261|               281|                                                                                                                                                                                                                  
                            2|                                                                                                                                                                                                                                            263                287                                                                                                                                                                                                                  
                            23                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    


Chain B from PDB  Type:PROTEIN  Length:471
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhh...hhhhhhh...........hhhhhhhhhhhhhhhhhhhhh.eeeeee..eeeeee.hhhhhhhhhh...............hhhhhhh....hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh...eeehhhhhhhhhhhhhhhhhh...........hhhhhhhhhhh................hhhhhhhhh.....hhhhhhhhhhhhhhhhh...........hhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhh.hhhhhhhhhhhhhhh.....eeee....eee..eee....eeeehhhhhhh...........hhhhhhhhhh...................hhhhhhhhhhhhhhhhhhheeee.......................eeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5te8 B   2 AYLYGTHSHGLFKKLGIPGPTPLPFLGNILSYHKGFCMFDMECHKKYGKVWGFYDGQQPVLAITDPDMIKTVLVKECYSVFTNRRPFGPVGFMKSAISIAEDEEWKRLRSLLSPTFTSGKLKEMVPIIAQYGDVLVRNLRREAETGKPVTLKDVFGAYSMDVITSTSFGVNIDSLNNPQDPFVENTKKLLRFDFLDPFFLSITVFPFLIPILEVLNICVFPREVTNFLRKSVKRMKESRLEDTQKHRVDFLQLMIDSQNSHKALSDLELVAQSIIFIFAGYETTSSVLSFIMYELATHPDVQQKLQEEIDAVLPNKAPPTYDTVLQMEYLDMVVNETLRLFPIAMRLERVCKKDVEINGMFIPKGVVVMIPSYALHRDPKYWTEPEKFLPERFSKKNKDNIDPYIYTPFGSGPRNCIGMRFALMNMKLALIRVLQNFSFKPCKETQIPLKLSLGGLLQPEKPVVLKVESRD 497
                            ||      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|      296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496 
                            2|                                                                                                                                                                                                                                                               281|                                                                                                                                                                                                                  
                            23                                                                                                                                                                                                                                                                287                                                                                                                                                                                                                  


Chain C from PDB  Type:PROTEIN  Length:469
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh....hhhhh............hhhhhhhhhhhhhhhhhhhhh.eeeeee..eeeeee.hhhhhhhhhh...............hhhhhh.....hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh........eehhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhh................hhhhhhhhhh....hhhhhhhhhhhhhhhh............hhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhh.hhhhhhhhhhhhhhh.....eeee....eee..eee....eeeehhhhhhh.................hhhhh..................hhhhhhhhhhhhhhhhhh...eee......................eeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5te8 C   2 AYLYGTHSHGLFKKLGIPGPTPLPFLGNILSYHKGFCMFDMECHKKYGKVWGFYDGQQPVLAITDPDMIKTVLVKECYSVFTNRRPFGPVGFMKSAISIAEDEEWKRLRSLLSPTFTSGKLKEMVPIIAQYGDVLVRNLRREAETGKPVTLKDVFGAYSMDVITSTSFGVNIDSLNNPQDPFVENTKKLLRFDFLDPFFLSITVFPFLIPILEVLNICVFPREVTNFLRKSVKRMKESRLEDTQKHRVDFLQLMIDSQNSKALSDLELVAQSIIFIFAGYETTSSVLSFIMYELATHPDVQQKLQEEIDAVLPNKAPPTYDTVLQMEYLDMVVNETLRLFPIAMRLERVCKKDVEINGMFIPKGVVVMIPSYALHRDPKYWTEPEKFLPERFSKKNKDNIDPYIYTPFGSGPRNCIGMRFALMNMKLALIRVLQNFSFKPCKETQIPLKLSLGGLLQPEKPVVLKVESR 496
                            ||      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|      297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487         
                            2|                                                                                                                                                                                                                                                               281|                                                                                                                                                                                                                
                            23                                                                                                                                                                                                                                                                288
   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 5TE8)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5TE8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5TE8)

(-) Gene Ontology  (41, 41)

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 Related Entries

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UniProtKB/Swiss-Prot
        CP3A4_HUMAN | P08684: 1tqn 1w0e 1w0f 1w0g 2j0d 2v0m 3nxu 3tjs 3ua1 4d6z 4d75 4d78 4d7d 4i3q 4i4g 4i4h 4k9t 4k9u 4k9v 4k9w 4k9x 4ny4 5a1p 5a1r 5g5j 5vc0 5vcc 5vcd 5vce 5vcg

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