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(-) Description

Title :  CRYSTAL STRUCTURE OF CYP2B6 (Y226H/K262R) IN COMPLEX WITH A MONOTERPENE BORNANE
 
Authors :  M. B. Shah, J. R. Halpert
Date :  24 Dec 16  (Deposition) - 12 Apr 17  (Release) - 31 May 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.93
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Oxidoreductase, Cytochrome P450, Cyp2B6 (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. B. Shah, J. Liu, Q. Zhang, C. D. Stout, J. R. Halpert
Halogen-Pi Interactions In The Cytochrome P450 Active Site: Structural Insights Into Human Cyp2B6 Substrate Selectivity
Acs Chem. Biol. V. 12 1204 2017
PubMed-ID: 28368100  |  Reference-DOI: 10.1021/ACSCHEMBIO.7B00056

(-) Compounds

Molecule 1 - CYTOCHROME P450 2B6
    Chains: A, B
    EC Number: 1.14.13.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: JM109
    Expression System Taxid: 562
    Gene: CYP2B6
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: 1,4-CINEOLE 2-EXO-MONOOXYGENASE,CYPIIB6,CYTOCHROME P450 IIB1

 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  (3, 10)

Asymmetric Unit (3, 10)
No.NameCountTypeFull Name
1CAE2Ligand/IonCAMPHANE
2CM56Ligand/Ion5-CYCLOHEXYL-1-PENTYL-BETA-D-MALTOSIDE
3HEM2Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
Biological Unit 1 (3, 5)
No.NameCountTypeFull Name
1CAE1Ligand/IonCAMPHANE
2CM53Ligand/Ion5-CYCLOHEXYL-1-PENTYL-BETA-D-MALTOSIDE
3HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
Biological Unit 2 (3, 5)
No.NameCountTypeFull Name
1CAE1Ligand/IonCAMPHANE
2CM53Ligand/Ion5-CYCLOHEXYL-1-PENTYL-BETA-D-MALTOSIDE
3HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:98 , VAL A:113 , TRP A:121 , ARG A:125 , MET A:132 , THR A:302 , THR A:303 , THR A:306 , LEU A:362 , LEU A:363 , VAL A:367 , HIS A:369 , LEU A:392 , PRO A:428 , PHE A:429 , SER A:430 , ARG A:434 , CYS A:436 , LEU A:437 , GLY A:438 , ALA A:442 , HOH A:718binding site for residue HEM A 501
02AC2SOFTWAREILE A:101 , ILE A:114 , PHE A:206binding site for residue CAE A 502
03AC3SOFTWAREPHE A:223binding site for residue CM5 A 503
04AC4SOFTWAREPHE A:188 , GLU A:194 , MET A:198 , PHE A:202 , ALA A:243 , TYR A:244 , PHE A:296 , LYS B:384binding site for residue CM5 A 504
05AC5SOFTWAREASP A:47 , ARG A:48 , VAL A:212binding site for residue CM5 A 505
06AC6SOFTWAREARG B:98 , VAL B:113 , ILE B:114 , TRP B:121 , ARG B:125 , MET B:132 , ALA B:298 , GLY B:299 , THR B:302 , THR B:303 , THR B:306 , LEU B:362 , LEU B:363 , VAL B:367 , HIS B:369 , LEU B:392 , PRO B:428 , PHE B:429 , SER B:430 , ARG B:434 , CYS B:436 , LEU B:437 , GLY B:438 , ALA B:442 , HOH B:762binding site for residue HEM B 501
07AC7SOFTWAREILE B:101 , ILE B:114 , PHE B:206 , VAL B:477binding site for residue CAE B 502
08AC8SOFTWAREPHE B:223binding site for residue CM5 B 503
09AC9SOFTWARELYS A:384 , GLU B:194 , MET B:198 , PHE B:202 , ILE B:241 , TYR B:244 , PHE B:296binding site for residue CM5 B 504
10AD1SOFTWAREARG B:48 , LEU B:51binding site for residue CM5 B 505

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5UDA)

(-) 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 ..............hhhhh...hhhhhhhhhhhhhh.eeeeee..eeeeee.hhhhhhhhhh.hhhhhhee.....hhhhhh.......hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhh.......ee....eee..eee....eeeehhhhhhh...........hhhhhh.......................hhhhhhhhhhhhhhhhhhheeee...hhhhh.....ee...ee......eeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5uda A  28 GKLPPGPRPLPLLGNLLQMDRRGLLKSFLRFREKYGDVFTVHLGPRPVVMLCGVEAIREALVDKAEAFSGRGKIAMVDPFFRGYGVIFANGNRWKVLRRFSVTTMRDFGRSVEERIQEEAQCLIEELRKSKGALMDPTFLFQSITANIICSIVFGKRFHYQDQEFLKMLNLFYQTFSLISSVFGQLFELFSGFLKHFPGAHRQVYKNLQEINAYIGHSVEKHRETLDPSAPRDLIDTYLLHMEKEKSNAHSEFSHQNLNLNTLSLFFAGTETTSTTLRYGFLLMLKYPHVAERVYREIEQVIGPHRPPELHDRAKMPYTEAVIYEIQRFSDLLPMGVPHIVTQHTSFRGYIIPKDTEVFLILSTALHDPHYFEKPDAFNPDHFLDANGALKKTEAFIPFSLGKRICLGEGIARAELFLFFTTILQNFSMASPVAPEDIDLTPQECGVGKIPPTYQIRFLPR 491
                                    37        47        57        67        77        87        97       107       117       127       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       480       490 
                                                                                                                                      136|                                                                                                                                                                                                                                                                                                                                                               
                                                                                                                                       140                                                                                                                                                                                                                                                                                                                                                               


Chain B from PDB  Type:PROTEIN  Length:460
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............hhhhh...hhhhhhhhhhhhhh.eeeeee..eeeeee.hhhhhhhhhh.hhhhhhee.....hhhhhh.......hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh...ee.hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhh.......ee....eee..eee....eeeehhhhhhh...........hhhhhh.......................hhhhhhhhhhhhhhhhhhheeee...hhhhh.....ee...ee.....eeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5uda B  28 GKLPPGPRPLPLLGNLLQMDRRGLLKSFLRFREKYGDVFTVHLGPRPVVMLCGVEAIREALVDKAEAFSGRGKIAMVDPFFRGYGVIFANGNRWKVLRRFSVTTMRDKRSVEERIQEEAQCLIEELRKSKGALMDPTFLFQSITANIICSIVFGKRFHYQDQEFLKMLNLFYQTFSLISSVFGQLFELFSGFLKHFPGAHRQVYKNLQEINAYIGHSVEKHRETLDPSAPRDLIDTYLLHMEKEKSNAHSEFSHQNLNLNTLSLFFAGTETTSTTLRYGFLLMLKYPHVAERVYREIEQVIGPHRPPELHDRAKMPYTEAVIYEIQRFSDLLPMGVPHIVTQHTSFRGYIIPKDTEVFLILSTALHDPHYFEKPDAFNPDHFLDANGALKKTEAFIPFSLGKRICLGEGIARAELFLFFTTILQNFSMASPVAPEDIDLTPQECGVGKIPPTYQIRFLPR 491
                                    37        47        57        67        77        87        97       107       117       127      |141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491
                                                                                                                                    134|                                                                                                                                                                                                                                                                                                                                                                
                                                                                                                                     139
   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 5UDA)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (22, 22)

Asymmetric Unit(hide GO term definitions)

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        CP2B6_HUMAN | P20813: 3ibd 3qoa 3qu8 3ua5 4i91 4rql 4rrt 4zv8 5uap 5uec 5ufg

(-) Related Entries Specified in the PDB File

5uec