4KTF | pdb_00004ktf

Crystal structure of Mycobacterium tuberculosis CYP121 in complex with 4,4'-(3-amino-1H-pyrazole-4,5-diyl)diphenol

PDB DOI: https://doi.org/10.2210/pdb4KTF/pdb

Classification: OXIDOREDUCTASE
Organism(s): Mycobacterium tuberculosis H37Rv
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2013-05-20 Released: 2013-07-03
Deposition Author(s): Hudson, S.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.35 Å
R-Value Free:
0.195 (Depositor), 0.194 (DCC)
R-Value Work:
0.166 (Depositor), 0.165 (DCC)
R-Value Observed:
0.168 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Overcoming the Limitations of Fragment Merging: Rescuing a Strained Merged Fragment Series Targeting Mycobacterium tuberculosis CYP121.

Hudson, S.A., Surade, S., Coyne, A.G., McLean, K.J., Leys, D., Munro, A.W., Abell, C.

(2013) ChemMedChem 8: 1451-1456

PubMed: 23788280 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1002/cmdc.201300219
Primary Citation Related Structures:
4KTF, 4KTJ, 4KTK, 4KTL

Organizational Affiliation

Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.

Macromolecule Content

Total Structure Weight: 44.44 kDa
Atom Count: 3,739
Modeled Residue Count: 393
Deposited Residue Count: 395
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome P450 121	A	395	Mycobacterium tuberculosis H37Rv	Mutation(s): 0 Gene Names: Rv2276, RVBD_2276 EC: 1.14

Small Molecules

Ligands 3 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]
1TM Query on 1TM Download:Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	4,4'-(3-amino-1H-pyrazole-4,5-diyl)diphenol C₁₅ H₁₃ N₃ O₂ SDULBSMUWSNMKJ-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A]	C [auth A], D [auth A], E [auth A], F [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.35 Å
R-Value Free: 0.195 (Depositor), 0.194 (DCC)
R-Value Work: 0.166 (Depositor), 0.165 (DCC)
R-Value Observed: 0.168 (Depositor)

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.2	α = 90
b = 78.2	β = 90
c = 263.191	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
REFMAC	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2013-07-03

Deposition Author(s):

Hudson, S.A.

Revision History (Full details and data files)

Version 1.0: 2013-07-03
Type: Initial release
Version 1.1: 2013-10-09
Changes: Database references
Version 1.2: 2017-11-15
Changes: Refinement description
Version 1.3: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description