3ATT

Crystal structure of Rv3168 with ATP

PDB DOI: https://doi.org/10.2210/pdb3ATT/pdb

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

Deposited: 2011-01-13 Released: 2011-08-03
Deposition Author(s): Kim, Y.-G., Kim, S., Nguyen, C.M.T., Kim, K.-J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.250
R-Value Work: 0.187
R-Value Observed: 0.190

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of Mycobacterium tuberculosis Rv3168: a putative aminoglycoside antibiotics resistance enzyme

Kim, S., Nguyen, C.M.T., Kim, E.-J., Kim, K.-J.

(2011) Proteins 79: 2983-2987

PubMed: 21905120 Search on PubMed
DOI: https://doi.org/10.1002/prot.23119
Primary Citation of Related Structures:
3ATS, 3ATT

Organizational Affiliation

Pohang Accelerator Laboratory, Pohang University of Science and Technology, Pohang, Kyungbuk, Korea.

Macromolecule Content

Total Structure Weight: 41.1 kDa
Atom Count: 3,074
Modelled Residue Count: 352
Deposited Residue Count: 357
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative uncharacterized protein	A	357	Mycobacterium tuberculosis	Mutation(s): 0 Gene Names: MT3257, Rv3168
UniProt
Find proteins for P9WI99 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WI99 Go to UniProtKB: P9WI99
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P9WI99
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ATP Query on ATP Download Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A]	H [auth A]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A]	G [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A]	E [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain F [auth A] MOL2 format, chain D [auth A] MOL2 format, chain F [auth A]	D [auth A], F [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain F [auth A] Interactions & Density Focus chain D [auth A] Focus chain F [auth A]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A]	B [auth A], C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.250
R-Value Work: 0.187
R-Value Observed: 0.190
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.876	α = 90
b = 62.104	β = 90
c = 103.265	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2011-08-03

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2011-08-03
Type: Initial release
Version 1.1: 2013-06-19
Changes: Database references
Version 1.2: 2017-10-11
Changes: Refinement description
Version 1.3: 2024-03-13
Changes: Data collection, Database references, Derived calculations

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Help and Resources

3ATT

Crystal structure of Rv3168 with ATP

Crystal structure of Mycobacterium tuberculosis Rv3168: a putative aminoglycoside antibiotics resistance enzyme

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)