5YK1

The complex structure of Rv3197-AMPPNP from Mycobacterium tuberculosis

• PDB DOI: https://doi.org/10.2210/pdb5YK1/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Mycobacterium tuberculosis H37Rv
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-10-11 Released: 2018-02-07 
• Deposition Author(s): Rao, Z.H., Zhang, Q.Q.
• Funding Organization(s): State Key Development Program for Basic Research of the Ministry of Science and Technology of China, National Natural Science Foundation of China

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.216 
• R-Value Work: 0.190 
• R-Value Observed: 0.192 

Starting Model: experimental

Literature

Discovery of the first macrolide antibiotic binding protein in Mycobacterium tuberculosis: a new antibiotic resistance drug target.

Zhang, Q., Liu, H., Liu, X., Jiang, D., Zhang, B., Tian, H., Yang, C., Guddat, L.W., Yang, H., Mi, K., Rao, Z.

(2018) Protein Cell 9: 971-975

• PubMed: 29350349 
• DOI: https://doi.org/10.1007/s13238-017-0502-7
• Primary Citation of Related Structures:  
  5YJZ, 5YK0, 5YK1, 5YK2

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Organizational Affiliation: 

College of Life Sciences, Nankai University, Tianjin, 300071, China.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 50.68 kDa 
• Atom Count: 3,390 
• Modelled Residue Count: 401 
• Deposited Residue Count: 452 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable conserved ATP-binding protein ABC transporter	A	452	Mycobacterium tuberculosis H37Rv	Mutation(s): 0  Gene Names: Rv3197
UniProt
Find proteins for O53343 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore O53343  Go to UniProtKB:  O53343

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ANP (Subject of Investigation/LOI)	B [auth A]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C10 H17 N6 O12 P3 PVKSNHVPLWYQGJ-KQYNXXCUSA-N
SO4	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	H [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.216 
• R-Value Work: 0.190 
• R-Value Observed: 0.192 
• Space Group: P 6₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 186.734	α = 90
b = 186.734	β = 90
c = 67.499	γ = 120

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-02-07 
Deposition Author(s): Rao, Z.H., Zhang, Q.Q.

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Funding Organization	Location	Grant Number
State Key Development Program for Basic Research of the Ministry of Science and Technology of China	China	2014CB542800
National Natural Science Foundation of China	China	81330036
National Natural Science Foundation of China	China	81520108019

Revision History  

• Version 1.0: 2018-02-07
  Type: Initial release
  
• Version 1.1: 2018-11-21
  Changes: Data collection, Database references
• Version 1.2: 2023-11-22
  Changes: Data collection, Database references, Refinement description