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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN CYP3A4 BOUND TO GLYCEROL
 
Authors :  I. Sevrioukova
Date :  31 Mar 17  (Deposition) - 31 May 17  (Release) - 28 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Biol. Unit 2:  A  (4x)
Keywords :  Cytochrome P450, Cyp3A4, Monooxygenase, Glycerol, Oxidoreductase (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.-, 1.14.13.157, 1.14.13.32, 1.14.14.1, 1.14.13.67, 1.14.13.97
    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, 21)

Asymmetric Unit (3, 21)
No.NameCountTypeFull Name
1EDO12Ligand/Ion1,2-ETHANEDIOL
2GOL8Ligand/IonGLYCEROL
3HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
Biological Unit 1 (3, 42)
No.NameCountTypeFull Name
1EDO24Ligand/Ion1,2-ETHANEDIOL
2GOL16Ligand/IonGLYCEROL
3HEM2Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
Biological Unit 2 (3, 84)
No.NameCountTypeFull Name
1EDO48Ligand/Ion1,2-ETHANEDIOL
2GOL32Ligand/IonGLYCEROL
3HEM4Ligand/IonPROTOPORPHYRIN IX CONTAINING FE

(-) Sites  (21, 21)

Asymmetric Unit (21, 21)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:105 , ILE A:118 , SER A:119 , TRP A:126 , ARG A:130 , PHE A:137 , PHE A:302 , ALA A:305 , GLY A:306 , 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 , MET A:452 , GOL A:602 , EDO A:611 , HOH A:788 , HOH A:798binding site for residue HEM A 601
02AC2SOFTWARESER A:119 , ARG A:212 , PHE A:304 , ALA A:305 , HEM A:601 , EDO A:612 , HOH A:798 , HOH A:813binding site for residue GOL A 602
03AC3SOFTWAREPRO A:41 , SER A:52 , PHE A:60 , GLU A:63 , LYS A:67 , TYR A:68binding site for residue GOL A 603
04AC4SOFTWARETHR A:42 , LEU A:44 , ASN A:49 , LEU A:51 , SER A:52 , EDO A:613 , HOH A:747 , HOH A:760binding site for residue GOL A 604
05AC5SOFTWAREGLY A:56 , PHE A:57 , CYS A:58 , MET A:371 , SER A:478 , GLY A:480 , GLY A:481 , LEU A:482 , LEU A:483 , GLN A:484 , HOH A:706binding site for residue GOL A 605
06AC6SOFTWAREILE A:50 , LEU A:51 , TYR A:53 , HIS A:54 , LEU A:216 , LEU A:221 , HOH A:714 , HOH A:830binding site for residue GOL A 606
07AC7SOFTWARELYS A:330 , GLU A:354 , MET A:358 , GLU A:417 , HOH A:705 , HOH A:834binding site for residue GOL A 607
08AC8SOFTWAREASP A:380 , GLU A:382 , PHE A:387 , HOH A:738binding site for residue GOL A 608
09AC9SOFTWAREPRO A:39 , PRO A:325 , GLN A:328 , GLN A:329 , GLN A:332 , SER A:464 , HOH A:741 , HOH A:870binding site for residue GOL A 609
10AD1SOFTWAREGLY A:40 , GLN A:329 , HOH A:725 , HOH A:757binding site for residue EDO A 610
11AD2SOFTWAREARG A:212 , HEM A:601 , HOH A:798binding site for residue EDO A 611
12AD3SOFTWAREPHE A:108 , SER A:119 , GOL A:602binding site for residue EDO A 612
13AD4SOFTWARELEU A:51 , GOL A:604binding site for residue EDO A 613
14AD5SOFTWARETRP A:408 , THR A:409 , ARG A:418 , EDO A:618binding site for residue EDO A 614
15AD6SOFTWARELYS A:173 , GLY A:177 , SER A:311binding site for residue EDO A 615
16AD7SOFTWAREGLN A:279binding site for residue EDO A 616
17AD8SOFTWARELEU A:351 , ASP A:357 , LYS A:453binding site for residue EDO A 617
18AD9SOFTWARETYR A:407 , TRP A:408 , ASP A:428 , EDO A:614binding site for residue EDO A 618
19AE1SOFTWAREILE A:184 , THR A:187 , SER A:188 , PHE A:271 , PHE A:302 , HOH A:799binding site for residue EDO A 619
20AE2SOFTWAREASP A:76 , GLY A:77 , GLN A:78 , GLN A:79 , THR A:224 , PRO A:227 , HOH A:740binding site for residue EDO A 620
21AE3SOFTWAREPHE A:367 , ARG A:403binding site for residue EDO A 621

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Gly A:109 -Pro A:110
2Leu A:261 -Glu A:262
3Ile A:473 -Pro A:474

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5VCC)

(-) 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:457
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhh...........hhhhhhhhhhhhhhhhhhhhh.eeeeee..eeeeee.hhhhhhhhhh...............hhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eehhhhhhhhhhhhhhhhhhh..........hhhhhhhh........hhhhhhhhhh..hhhhhhhh.....hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.....eeee....eee..eee....eeeehhhhhhh...........hhhhhh..hhhhh................hhhhhhhhhhhhhhhhhhheeeee......................eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5vcc A  29 SHGLFKKLGIPGPTPLPFLGNILSYHKGFCMFDMECHKKYGKVWGFYDGQQPVLAITDPDMIKTVLVKECYSVFTNRRPFGPVGFMKSAISIAEDEEWKRLRSLLSPTFTSGKLKEMVPIIAQYGDVLVRNLRREAETGKPVTLKDVFGAYSMDVITSTSFGVNIDSLNNPQDPFVENTKKLLRFDFLDPFFLSITVFPFLIPILEVLNICVFPREVTNFLRKSVKRMKESRLEDVDFLQLMIDSQNSKALSDLELVAQSIIFIFAGYETTSSVLSFIMYELATHPDVQQKLQEEIDAVLPNKAPPTYDTVLQMEYLDMVVNETLRLFPIAMRLERVCKKDVEINGMFIPKGVVVMIPSYALHRDPKYWTEPEKFLPERFSKKNKDNIDPYIYTPFGSGPRNCIGMRFALMNMKLALIRVLQNFSFKPCKETQIPLKLSLGGLLQPEKPVVLKVESR 496
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258    || 273       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       
                                                                                                                                                                                                                                                                    263|         281|                                                                                                                                                                                                                
                                                                                                                                                                                                                                                                     269          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 5VCC)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (41, 41)

Asymmetric Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Gly A:109 - Pro A:110   [ RasMol ]  
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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 5vcd 5vce 5vcg

(-) Related Entries Specified in the PDB File

5vc0 5vcd 5vce 5vcg