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(-) Description

Title :  CRYSTAL STRUCTURE OF THE CYSTEINE DEPLETED CYP3A4 BOUND TO BROMOERGOCRYPTINE
 
Authors :  I. Sevrioukova
Date :  31 Mar 17  (Deposition) - 31 May 17  (Release) - 28 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Biol. Unit 2:  A  (4x)
Keywords :  Cytochrome P450, Cyp3A4, Monooxygenase, Cysteine Mutation, Bromoergocryprine, Oxidoreductase-Substrate Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  I. F. Sevrioukova
High-Level Production And Properties Of The Cysteine-Depleted Cytochrome P450 3A4.
Biochemistry V. 56 3058 2017
PubMed-ID: 28590129  |  Reference-DOI: 10.1021/ACS.BIOCHEM.7B00334

(-) Compounds

Molecule 1 - CYTOCHROME P450 3A4
    Chains: A
    EC Number: 1.14.13.157, 1.14.13.32, 1.14.13.67, 1.14.13.9
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: CYP3A4, CYP3A3
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    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

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A
Biological Unit 2 (4x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric Unit (3, 6)
No.NameCountTypeFull Name
108Y1Ligand/IonBROMOERGOCRYPTINE
2GOL4Ligand/IonGLYCEROL
3HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
Biological Unit 1 (3, 12)
No.NameCountTypeFull Name
108Y2Ligand/IonBROMOERGOCRYPTINE
2GOL8Ligand/IonGLYCEROL
3HEM2Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
Biological Unit 2 (3, 24)
No.NameCountTypeFull Name
108Y4Ligand/IonBROMOERGOCRYPTINE
2GOL16Ligand/IonGLYCEROL
3HEM4Ligand/IonPROTOPORPHYRIN IX CONTAINING FE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:105 , ILE A:118 , TRP A:126 , ARG A:130 , PHE A:137 , THR A:309 , VAL A:313 , ILE A:369 , ALA A:370 , 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 , 08Y A:602binding site for residue HEM A 601
2AC2SOFTWAREPHE A:57 , ARG A:105 , PHE A:108 , SER A:119 , ARG A:212 , PHE A:215 , THR A:224 , PHE A:304 , ALA A:305 , ALA A:370 , ARG A:372 , HEM A:601binding site for residue 08Y A 602
3AC3SOFTWARETYR A:407 , TRP A:408 , THR A:409 , ARG A:418 , GOL A:605binding site for residue GOL A 603
4AC4SOFTWAREPHE A:33 , ILE A:38 , GLY A:40 , THR A:42 , HOH A:707 , HOH A:711 , HOH A:735binding site for residue GOL A 604
5AC5SOFTWARELYS A:406 , TYR A:407 , GOL A:603binding site for residue GOL A 605
6AC6SOFTWARELYS A:55 , GLY A:56 , PHE A:57 , ALA A:58 , MET A:59 , MET A:371 , LEU A:477 , SER A:478 , GLY A:480 , LEU A:482 , LEU A:483binding site for residue GOL A 606

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Ile A:473 -Pro A:474

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5VCG)

(-) 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:461
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhh............hhhhhhhhhhhhhhhhhhhhh.eeeeee..eeeeee.hhhhhhhhhh...............hhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eehhhhhhhhhhhhhhhhhh...........hhhhhhhhhh......hhhhhhhhhh..hhhhhhhh.....hhhhhhhhhhhhhhhhhh.......hhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhh.hhhhhhhhhhhhhhh.....eeee....eee..eee....eeeehhhhhhh...........hhhhhh.......................hhhhhhhhhhhhhhhhhhheeeee......................eeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5vcg A  28 HSHGLFKKLGIPGPTPLPFLGNILSYHKGFAMFDMEMHKKYGKVWGFYDGQQPVLAITDPDMIKTVLVKEAYSVFTNRRPFGPVGFMKSAISIAEDEEWKRLRSLLSPTFTSGKLKEMVPIIAQYGDVLVRNLRREAETGKPVTLKDVFGAYSMDVITSTSFGVNIDSLNNPQDPFVENTKKLLRFDFLDPFFLSITVFPFLIPILEVLNITVFPREVTNFLRKSVKRMKESRLEDHRVDFLQLMIDSQNSKALSDLELVAQSIIFIFAGYETTSSVLSFIMYELATHPDVQQKLQEEIDAVLPNKAPPTYDTVLQMEYLDMVVNETLRLFPIAMRLERVAKKDVEINGMFIPKGVVVMIPSYALHRDPKYWTEPEKFLPERFSKKNKDNIDPYIYTPFGSGPRNCIGMRFALMNMKLALIRVLQNFSFKPSKETQIPLKLSLGGLLQPEKPVVLKVESRD 497
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257     ||270       280||     296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496 
                                                                                                                                                                                                                                                                     263|           281|                                                                                                                                                                                                                 
                                                                                                                                                                                                                                                                      267            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 5VCG)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (41, 41)

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 Related Entries

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

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 5te8 5vc0 5vcc 5vcd 5vce

(-) Related Entries Specified in the PDB File

5vc0 5vcc 5vcd 5vce