3PYG

Mycobacterium tuberculosis 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase (IspE) in complex with ADP

PDB DOI: https://doi.org/10.2210/pdb3PYG/pdb

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

Deposited: 2010-12-13 Released: 2012-01-25
Deposition Author(s): Shan, S., Chen, X.H., Liu, T., Zhao, H.C., Rao, Z.H., Lou, Z.Y.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.99 Å
R-Value Free:
0.263 (Depositor), 0.260 (DCC)
R-Value Work:
0.220 (Depositor), 0.220 (DCC)
R-Value Observed:
0.222 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

The Structural Basis for anti-TB Drug Discovery targeting of 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase (IspE) from Mycobacterium tuberculosis

Shan, S., Chen, X.H., Liu, T., Zhao, H.C., Rao, Z.H., Lou, Z.Y.

To be published.

Macromolecule Content

Total Structure Weight: 31.84 kDa
Atom Count: 2,352
Modelled Residue Count: 298
Deposited Residue Count: 306
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
4-diphosphocytidyl-2-C-methyl-D-erythritol kinase	A	306	Mycobacterium tuberculosis	Mutation(s): 0 Gene Names: ispE, Rv1011, MT1040, MTCI237.28 EC: 2.7.1.148
UniProt
Find proteins for P9WKG7 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WKG7 Go to UniProtKB: P9WKG7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P9WKG7
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADP Query on ADP 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]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.99 Å
R-Value Free: 0.263 (Depositor), 0.260 (DCC)
R-Value Work: 0.220 (Depositor), 0.220 (DCC)
R-Value Observed: 0.222 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.199	α = 90
b = 73.122	β = 90
c = 106.958	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2012-01-25

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-01-25
Type: Initial release
Version 1.1: 2024-03-20
Changes: Data collection, Database references, Derived calculations

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.