5WP2

1.44 Angstrom crystal structure of CYP121 from Mycobacterium tuberculosis in complex with substrate and CN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.439 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.179 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Probing Ligand Exchange in the P450 Enzyme CYP121 from Mycobacterium tuberculosis: Dynamic Equilibrium of the Distal Heme Ligand as a Function of pH and Temperature.

Fielding, A.J.Dornevil, K.Ma, L.Davis, I.Liu, A.

(2017) J. Am. Chem. Soc. 139: 17484-17499


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Mycocyclosin synthase
A
395Mycobacterium tuberculosisMutation(s): 0 
Gene Names: cyp121 (cyp121_1)
EC: 1.14.-.-
Find proteins for A0A0T9WNE5 (Mycobacterium tuberculosis)
Go to UniProtKB:  A0A0T9WNE5
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
YTT
Query on YTT

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Download CCD File 
A
(3S,6S)-3,6-bis(4-hydroxybenzyl)piperazine-2,5-dione
cyclo(tyrosyl-tyrosyl), Cyclo(tyr-tyr)
C18 H18 N2 O4
NGPCLOGFGKJCBP-HOTGVXAUSA-N
 Ligand Interaction
CYN
Query on CYN

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Download CCD File 
A
CYANIDE ION
C N
XFXPMWWXUTWYJX-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
HEM
Query on HEM

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Download CCD File 
A
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.439 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.179 
  • Space Group: P 65 2 2
Unit Cell:
Length (Å)Angle (°)
a = 77.856α = 90.00
b = 77.856β = 90.00
c = 263.615γ = 120.00
Software Package:
Software NamePurpose
DENZOdata collection
SCALEPACKdata scaling
DENZOdata reduction
PHENIXrefinement
PDB_EXTRACTdata extraction
PHENIXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM108988
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM107529

Revision History 

  • Version 1.0: 2018-05-30
    Type: Initial release