5B2X

Crystal Structure of P450BM3 mutant with N-perfluoroheptanoyl-L-tryptophan


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.181 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Crystal Structure of P450BM3 with decoy molecules

Cong, Z.Shoji, O.Kasai, C.Sugimoto, H.Shiro, Y.Watanabe, Y.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bifunctional cytochrome P450/NADPH--P450 reductase
A, B
456Priestia megateriumMutation(s): 1 
Gene Names: cyp102A1cyp102
EC: 1.14.14.1 (PDB Primary Data), 1.6.2.4 (PDB Primary Data)
UniProt
Find proteins for P14779 (Priestia megaterium (strain ATCC 14581 / DSM 32 / CCUG 1817 / JCM 2506 / NBRC 15308 / NCIMB 9376 / NCTC 10342 / NRRL B-14308 / VKM B-512 / Ford 19))
Explore P14779 
Go to UniProtKB:  P14779
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP14779
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download Ideal Coordinates CCD File 
C [auth A],
F [auth B]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
W0T
Query on W0T

Download Ideal Coordinates CCD File 
D [auth A](2~{S})-3-(1~{H}-indol-3-yl)-2-[2,2,3,3,4,4,5,5,6,6,7,7,7-tridecakis(fluoranyl)heptanoylamino]propanoic acid
C18 H11 F13 N2 O3
VIATWFKQWKXLPP-JTQLQIEISA-N
DMS
Query on DMS

Download Ideal Coordinates CCD File 
E [auth A],
G [auth B]
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.181 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.402α = 90
b = 147.355β = 100.1
c = 64.301γ = 90
Software Package:
Software NamePurpose
DENZOdata collection
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
The Ministry of Education, Culture, Sports, Science, and TechnologyJapan24225004
The Ministry of Education, Culture, Sports, Science, and TechnologyJapan15H05806
The Japan Science and Technology Agency (JST)Japan15658843

Revision History  (Full details and data files)

  • Version 1.0: 2017-02-08
    Type: Initial release
  • Version 1.1: 2020-02-26
    Changes: Data collection
  • Version 1.2: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description