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(-) Description

Title :  STRUCTURE OF CYP2B4 F244W IN A LIGAND FREE CONFORMATION
 
Authors :  M. B. Shah, C. D. Stout, J. R. Halpert
Date :  05 Nov 15  (Deposition) - 23 Mar 16  (Release) - 01 Jun 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.02
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Cytochrome P450, Monooxygenase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Liu, M. B. Shah, Q. Zhang, C. D. Stout, J. R. Halpert, P. R. Wilderman
Coumarin Derivatives As Substrate Probes Of Mammalian Cytochromes P450 2B4 And 2B6: Assessing The Importance Of 7-Alkoxy Chain Length, Halogen Substitution, And Non-Active Site Mutations.
Biochemistry V. 55 1997 2016
PubMed-ID: 26982502  |  Reference-DOI: 10.1021/ACS.BIOCHEM.5B01330

(-) Compounds

Molecule 1 - CYTOCHROME P450 2B4
    Chains: A, B
    EC Number: 1.14.14.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PKK
    Expression System Strain: TOPP3
    Expression System Taxid: 562
    Gene: CYP2B4
    Mutation: YES
    Organism Common: RABBIT
    Organism Scientific: ORYCTOLAGUS CUNICULUS
    Organism Taxid: 9986
    Synonym: CYPIIB4,CYTOCHROME P450 ISOZYME 2,CYTOCHROME P450 LM2, CYTOCHROME P450 TYPE B0,CYTOCHROME P450 TYPE B1

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 6)
No.NameCountTypeFull Name
1CM54Ligand/Ion5-CYCLOHEXYL-1-PENTYL-BETA-D-MALTOSIDE
2HEM2Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
1CM52Ligand/Ion5-CYCLOHEXYL-1-PENTYL-BETA-D-MALTOSIDE
2HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
1CM52Ligand/Ion5-CYCLOHEXYL-1-PENTYL-BETA-D-MALTOSIDE
2HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:98 , VAL A:113 , ILE A:114 , TRP A:121 , ARG A:125 , GLY A:299 , THR A:303 , ILE A:363 , VAL A:367 , HIS A:369 , PRO A:428 , PHE A:429 , SER A:430 , ARG A:434 , CYS A:436 , LEU A:437 , GLY A:438 , ALA A:442binding site for residue HEM A 501
2AC2SOFTWARELYS A:186 , PHE A:188 , VAL A:194 , PHE A:195 , LEU A:198 , LEU A:199 , PHE A:202 , TRP A:244 , ASP A:467binding site for residue CM5 A 502
3AC3SOFTWARELEU A:44 , MET A:46 , ASP A:47 , ARG A:48 , GLY A:50binding site for residue CM5 A 503
4AC4SOFTWAREARG B:98 , TRP B:121 , ARG B:125 , ALA B:298 , GLY B:299 , THR B:303 , ILE B:363 , VAL B:367 , HIS B:369 , PRO B:428 , PHE B:429 , SER B:430 , ARG B:434 , CYS B:436 , LEU B:437 , GLY B:438 , ALA B:442binding site for residue HEM B 501
5AC5SOFTWARELEU B:44 , ASP B:47binding site for residue CM5 B 502
6AC6SOFTWAREPHE B:188 , VAL B:194 , PHE B:195 , LEU B:198 , LEU B:199 , PHE B:202 , TRP B:244 , ASP B:467binding site for residue CM5 B 503

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5EM4)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5EM4)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5EM4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5EM4)

(-) Exons   (0, 0)

(no "Exon" information available for 5EM4)

(-) 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 ...........hhhhhhh...hhhhhhhhhhhhhh.eeeeee..eeeeee.hhhhhhhhhh.......ee.....hhhhhh.......hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhh..hhhhhhhhhhhhhhhh.......ee....eee..eee....eee..hhhhhh...........hhhhhh.........................hhhhhhhhhhhhhhhhheeee...hhhhh................eeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5em4 A  29 KLPPGPSPLPVLGNLLQMDRKGLLRSFLRLREKYGDVFTVYLGSRPVVVLCGTDAIREALVDQAEAFSGRGKIAVVDPIFQGYGVIFANGERWRALRRFSLATMRDFGKRSVEERIQEEARCLVEELRKSKGALLDNTLLFHSITSNIICSIVFGKRFDYKDPVFLRLLDLFFQSFSLISSFSSQVFELFSGFLKYFPGTHRQIYRNLQEINTWIGQSVEKHRATLDPSNPRDFIDVYLLRMEKDKSDPSSEFHHQNLILTVLSLFFAGTETTSTTLRYGFLLMLKYPHVTERVQKEIEQVIGSHRPPALDDRAKMPYTDAVIHEIQRLGDLIPFGVPHTVTKDTQFRGYVIPKNTEVFPVLSSALHDPRYFETPNTFNPGHFLDANGALKRNEGFMPFSLGKRICLGEGIARTELFLFFTTILQNFSIASPVPPEDIDLTPSGVGNVPPSYQIRFLARH 492
                                    38        48        58        68        78        88        98       108       118       128       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 ||    482       492
                                                                                                                                     136|                                                                                                                                                                                                                                                                                                                                          472|                 
                                                                                                                                      139                                                                                                                                                                                                                                                                                                                                           475                 


Chain B from PDB  Type:PROTEIN  Length:459
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............hhhhhh...hhhhhhhhhhhhhh.eee.......eeeeehhhhhhhhhh.......ee.....hhhhhh.......hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhh..hhhhhhhhhhhhhhhh.......ee....eee..eee....eeeeehhhhhh...........hhhhhh.........................hhhhhhhhhhhhhhhhheeee...hhhhh................eeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5em4 B  29 KLPPGPSPLPVLGNLLQMDRKGLLRSFLRLREKYGDVFTVYLGSRPVVVLCGTDAIREALVDQAEAFSGRGKIAVVDPIFQGYGVIFANGERWRALRRFSLATMRDFGKRSVEERIQEEARCLVEELRKSKGALLDNTLLFHSITSNIICSIVFGKRFDYKDPVFLRLLDLFFQSFSLISSFSSQVFELFSGFLKYFPGTHRQIYRNLQEINTWIGQSVEKHRATLDPSNPRDFIDVYLLRMEKDKDPSSEFHHQNLILTVLSLFFAGTETTSTTLRYGFLLMLKYPHVTERVQKEIEQVIGSHRPPALDDRAKMPYTDAVIHEIQRLGDLIPFGVPHTVTKDTQFRGYVIPKNTEVFPVLSSALHDPRYFETPNTFNPGHFLDANGALKRNEGFMPFSLGKRICLGEGIARTELFLFFTTILQNFSIASPVPPEDIDLTPSGVGNVPPSYQIRFLARH 492
                                    38        48        58        68        78        88        98       108       118       128       140       150       160       170       180       190       200       210       220       230       240       250       260       270     ||281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471||     483         
                                                                                                                                     136|                                                                                                                                      276|                                                                                                                                                                                               472|                 
                                                                                                                                      139                                                                                                                                       278                                                                                                                                                                                                475
   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  (0, 0)

(no "SCOP Domain" information available for 5EM4)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5EM4)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5EM4)

(-) Gene Ontology  (14, 14)

Asymmetric Unit(hide GO term definitions)

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  5em4
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  CP2B4_RABIT | P00178
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  1.14.14.1
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 Related Entries

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

UniProtKB/Swiss-Prot
        CP2B4_RABIT | P00178: 1po5 1suo 2bdm 2q6n 3g5n 3g93 3kw4 3me6 3mvr 3r1a 3r1b 3tk3 3tmz 3uas 4h1n 4jlt 4mgj 5iut 5iuz

(-) Related Entries Specified in the PDB File

1po5 SAME PROTEIN IN A LIGAND FREE STATE - OPEN CONFORMATION
1suo SAME PROTEIN COMPLEXED WITH 4-(4-CHLOROPHENYL)IMIDAZOLE
2bdm SAME PROTEIN COMPLEXED WITH BIFONAZOLE
2q6n SAME PROTEIN COMPLEXED WITH 1-(4-CHLOROPHENYL)IMIDAZOLE
3g5n SAME PROTEIN COMPLEXED WITH 1-BIPHENYL-4-METHYL-1H-IMIDAZOLE
3g93 SAME PROTEIN COMPLEXED WITH 1-BIPHENYL-4-METHYL-1H-IMIDAZOLE
3kw4 SAME PROTEIN COMPLEXED WITH TICLOPIDINE
3me6 SAME PROTEIN COMPLEXED WITH CLOPIDOGREL
3mvr SAME PROTEIN IN A LIGAND FREE STATE - CLOSE CONFORMATION
3r1a SAME PROTEIN COMPLEXED WITH TERT-BUTYLPHENYLACETYLENE
3r1b SAME PROTEIN COMPLEXED WITH TERT-BUTYLPHENYLACETYLENE
3tk3 SAME PROTEIN (L437A) COMPLEXED WITH 4-(4-CHLOROPHENYL)IMIDAZOLE
3tmz SAME PROTEIN COMPLEXED WITH AMLODIPINE
3uas SAME PROTEIN COMPLEXED WITH 9-ETHYNYLPHENANTHRENE
4h1n SAME PROTEIN (F297A) COMPLEXED WITH CLOPIDOGREL
4jlt SAME PROTEIN COMPLEXED WITH PAROXETINE