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), 0.237 (DCC)
R-Value Work:
0.190 (Depositor), 0.194 (DCC)
R-Value Observed:
0.192 (Depositor)

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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

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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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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), 0.237 (DCC)
R-Value Work: 0.190 (Depositor), 0.194 (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

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Ligand Structure Quality Assessment

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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

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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.