6O7F | pdb_00006o7f

Mycobacterium tuberculosis L-alanine dehydrogenase x-ray structure in complex with N6-isobutyl adenosine

PDB DOI: https://doi.org/10.2210/pdb6O7F/pdb

Classification: OXIDOREDUCTASE
Organism(s): Mycobacterium tuberculosis H37Rv
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2019-03-07 Released: 2020-09-09
Deposition Author(s): Kim, H.-B., Hung, L.-W., Terwilliger, T.C., Kim, C.-Y., Structures of Mtb Proteins Conferring Susceptibility to Known Mtb Inhibitors (MTBI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.234 (Depositor), 0.240 (DCC)
R-Value Work:
0.190 (Depositor), 0.190 (DCC)
R-Value Observed:
0.192 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Mycobacterium tuberculosis L-alanine dehydrogenase x-ray structure in complex with N6-isobutyl adenosine

Kim, H.-B., Hung, L.-W., Terwilliger, T.C., Kim, C.-Y.

To be published.

Macromolecule Content

Total Structure Weight: 39.09 kDa
Atom Count: 2,857
Modeled Residue Count: 371
Deposited Residue Count: 371
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alanine dehydrogenase	A	371	Mycobacterium tuberculosis H37Rv	Mutation(s): 0 Gene Names: ald, Rv2780, MTV002.45 EC: 1.4.1.1
UniProt
Find proteins for P9WQB1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WQB1 Go to UniProtKB: P9WQB1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P9WQB1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NKV Query on NKV 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]	N-(2-methylpropanoyl)adenosine C₁₄ H₁₉ N₅ O₅ RSLAEWMJDPSZPS-AKAIJSEGSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.234 (Depositor), 0.240 (DCC)
R-Value Work: 0.190 (Depositor), 0.190 (DCC)
R-Value Observed: 0.192 (Depositor)

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.423	α = 90
b = 88.423	β = 90
c = 289.991	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2020-09-09

Deposition Author(s):

Terwilliger, T.C.

Structures of Mtb Proteins Conferring Susceptibility to Known Mtb Inhibitors (MTBI)

Revision History (Full details and data files)

Version 1.0: 2020-09-09
Type: Initial release
Version 1.1: 2024-03-13
Changes: Data collection, Database references

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.