6UPG | pdb_00006upg

Crystal structure of Mycobacterium tuberculosis CYP121 in complex with cYF-4-OMe

PDB DOI: https://doi.org/10.2210/pdb6UPG/pdb

Classification: OXIDOREDUCTASE
Organism(s): Mycobacterium tuberculosis
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2019-10-17 Released: 2020-04-29
Deposition Author(s): Nguyen, R.C.D., Yang, Y., Liu, A.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.39 Å
R-Value Free:
0.195 (Depositor), 0.196 (DCC)
R-Value Work:
0.185 (Depositor), 0.187 (DCC)
R-Value Observed:
0.186 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

Substrate-Assisted Hydroxylation and O-Demethylation in the Peroxidase-like Cytochrome P450 Enzyme CYP121

Nguyen, R.C., Yang, Y., Davis, I., Liu, A.

(2020) ACS Catal 10: 1628-1639

DOI: https://doi.org/10.1021/acscatal.9b04596

Macromolecule Content

Total Structure Weight: 44.13 kDa
Atom Count: 3,627
Modeled Residue Count: 395
Deposited Residue Count: 395
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mycocyclosin synthase	A	395	Mycobacterium tuberculosis	Mutation(s): 0 Gene Names: cyp121, MT2336 EC: 1.14.19.70
UniProt
Find proteins for P9WPP7 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WPP7 Go to UniProtKB: P9WPP7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P9WPP7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM Query on HEM Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
KEQ (Subject of Investigation/LOI) Query on KEQ Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	(3~{S},6~{S})-3-[(4-hydroxyphenyl)methyl]-6-[(4-methoxyphenyl)methyl]piperazine-2,5-dione C₁₉ H₂₀ N₂ O₄ SXIBGFQFSYRUSU-IRXDYDNUSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
KEQ	BindingDB: 6UPG	Kd: 1.04e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.39 Å
R-Value Free: 0.195 (Depositor), 0.196 (DCC)
R-Value Work: 0.185 (Depositor), 0.187 (DCC)
R-Value Observed: 0.186 (Depositor)

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.46	α = 90
b = 77.46	β = 90
c = 262.588	γ = 120

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
PHENIX	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2020-04-29

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01GM108988

Revision History (Full details and data files)

Version 1.0: 2020-04-29
Type: Initial release
Version 1.1: 2023-10-11
Changes: Data collection, Database references, Refinement description

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.