3ORP

Mycobacterium tuberculosis PknB kinase domain L33D mutant (crystal form 5)

PDB DOI: https://doi.org/10.2210/pdb3ORP/pdb

Classification: TRANSFERASE
Organism(s): Mycobacterium tuberculosis H37Ra
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2010-09-07 Released: 2010-12-15
Deposition Author(s): Good, M.C., Echols, N., Lombana, T.N., Alber, T., TB Structural Genomics Consortium (TBSGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.238
R-Value Work: 0.188
R-Value Observed: 0.191

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

Allosteric activation mechanism of the Mycobacterium tuberculosis receptor Ser/Thr kinase, PknB

Lombana, T.N., Echols, N., Good, M.C., Thomsen, N.D., Ng, H.-L., Greenstein, A.E., Falick, A.M., King, D.S., Alber, T.

(2010) Structure 18: 1667-1677

Macromolecule Content

Total Structure Weight: 34.04 kDa
Atom Count: 2,242
Modelled Residue Count: 274
Deposited Residue Count: 311
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine protein kinase	A	311	Mycobacterium tuberculosis H37Ra	Mutation(s): 1 Gene Names: MRA_0016, pknB, PknB (Rv0014c) EC: 2.7.11.1
UniProt
Find proteins for P9WI81 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WI81 Go to UniProtKB: P9WI81
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P9WI81
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AGS Query on AGS 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]	PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER C₁₀ H₁₆ N₅ O₁₂ P₃ S NLTUCYMLOPLUHL-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: 2.10 Å
R-Value Free: 0.238
R-Value Work: 0.188
R-Value Observed: 0.191
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.185	α = 90
b = 52.164	β = 90
c = 155.652	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
EPMR	phasing
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2010-12-15

Deposition Author(s):

TB Structural Genomics Consortium (TBSGC)

Revision History (Full details and data files)

Version 1.0: 2010-12-15
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2021-10-06
Changes: Database references, Derived calculations
Version 1.3: 2023-09-06
Changes: Data collection, Refinement description

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.