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(-) Description

Title :  CRYSTAL STRUCTURE OF THE CYSTEINE DEPLETED 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 :  1.95
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Biol. Unit 2:  A  (4x)
Keywords :  Cytochrome P450, Cyp3A4, Monooxygenase, Cysteine Mutation, 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: 1.14.13.157, 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  (2, 13)

Asymmetric Unit (2, 13)
No.NameCountTypeFull Name
1GOL12Ligand/IonGLYCEROL
2HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
Biological Unit 1 (2, 26)
No.NameCountTypeFull Name
1GOL24Ligand/IonGLYCEROL
2HEM2Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
Biological Unit 2 (2, 52)
No.NameCountTypeFull Name
1GOL48Ligand/IonGLYCEROL
2HEM4Ligand/IonPROTOPORPHYRIN IX CONTAINING FE

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
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 , THR A:309 , ILE A:369 , 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 , HOH A:721 , HOH A:764binding site for residue HEM A 601
02AC2SOFTWARESER A:119 , ARG A:212 , PHE A:304 , ALA A:305 , HOH A:721 , HOH A:727 , HOH A:765binding site for residue GOL A 602
03AC3SOFTWAREPHE A:33 , GLY A:40 , THR A:42 , GLN A:329 , HOH A:708 , HOH A:716 , HOH A:725binding site for residue GOL A 603
04AC4SOFTWAREPRO A:41 , THR A:42 , LEU A:44 , ASN A:49 , LEU A:51 , SER A:52 , HOH A:733 , HOH A:750binding site for residue GOL A 604
05AC5SOFTWARELYS A:55 , GLY A:56 , PHE A:57 , ALA A:58 , MET A:59 , MET A:371 , SER A:478 , GLY A:480 , LEU A:482 , LEU A:483binding site for residue GOL A 605
06AC6SOFTWARETYR A:53 , PHE A:57 , ASP A:76 , ARG A:106 , PHE A:215 , PHE A:220 , THR A:224 , ARG A:372binding site for residue GOL A 606
07AC7SOFTWARETYR A:407 , THR A:409 , ARG A:418binding site for residue GOL A 607
08AC8SOFTWARELYS A:34 , LYS A:35 , HIS A:324 , PRO A:325 , ASP A:326 , HOH A:735binding site for residue GOL A 608
09AC9SOFTWARELYS A:330 , GLU A:354 , MET A:358 , GLU A:417binding site for residue GOL A 609
10AD1SOFTWARELYS A:209 , LEU A:210 , LEU A:211 , PHE A:213 , PRO A:242binding site for residue GOL A 610
11AD2SOFTWARELYS A:67 , GLN A:332 , GLU A:333 , ARG A:496binding site for residue GOL A 611
12AD3SOFTWAREPRO A:405 , LYS A:406 , TYR A:407 , THR A:409binding site for residue GOL A 612
13AD4SOFTWAREGLU A:308 , SER A:311 , SER A:312 , GLN A:484 , PRO A:485binding site for residue GOL A 613

(-) SS Bonds  (0, 0)

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

(-) 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 5VCD)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5VCD)

(-) 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:460
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhh.eeeeee..eeeeee.hhhhhhhhhh................hhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhhhhhhhhhh...........hhhhhhhh........hhhhhhhhhh..hhhhhhhh.....hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhh.hhhhhhhhhhhhhhh.....eeee....eee..eee....eeeehhhhhhh...........hhhhhh..hhhhh................hhhhhhhhhhhhhhhhhhheeeee......................eeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5vcd A  26 GTHSHGLFKKLGIPGPTPLPFLGNILSYHKGFAMFDMEMHKKYGKVWGFYDGQQPVLAITDPDMIKTVLVKEAYSVFTNRRPFGPVGFMKSAISIAEDEEWKRLRSLLSPTFTSGKLKEMVPIIAQYGDVLVRNLRREAETGKPVTLKDVFGAYSMDVITSTSFGVNIDSLNNPQDPFVENTKKLLRFDFLDPFFLSITVFPFLIPILEVLNITVFPREVTNFLRKSVKRMKESRLEDVDFLQLMIDSQNSKALSDLELVAQSIIFIFAGYETTSSVLSFIMYELATHPDVQQKLQEEIDAVLPNKAPPTYDTVLQMEYLDMVVNETLRLFPIAMRLERVAKKDVEINGMFIPKGVVVMIPSYALHRDPKYWTEPEKFLPERFSKKNKDNIDPYIYTPFGSGPRNCIGMRFALMNMKLALIRVLQNFSFKPSKETQIPLKLSLGGLLQPEKPVVLKVESR 496
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       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|                                                                                                                                                                                                                
                                                                                                                                                                                                                                                                        269          288
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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 5VCD)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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

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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 5te8 5vc0 5vcc 5vce 5vcg

(-) Related Entries Specified in the PDB File

5vc0 5vcc 5vce 5vcg