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

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

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

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

Organizational Affiliation

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

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

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O53343
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ANP (Subject of Investigation/LOI) Query on ANP Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C₁₀ H₁₇ N₆ O₁₂ P₃ PVKSNHVPLWYQGJ-KQYNXXCUSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A]	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A]	H [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]

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

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2018-02-07

Deposition Author(s):

Rao, Z.H.

Zhang, Q.Q.

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 (Full details and data files)

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

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Help and Resources

5YK1

The complex structure of Rv3197-AMPPNP from Mycobacterium tuberculosis

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

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)