6CYZ

Mycobacterial homoserine kinase ThrB in complex with AMPPNP

PDB DOI: https://doi.org/10.2210/pdb6CYZ/pdb

Classification: TRANSFERASE
Organism(s): Mycobacteroides abscessus ATCC 19977
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2018-04-07 Released: 2018-04-18
Deposition Author(s): Li, J., Korotkov, K.V.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.04 Å
R-Value Free: 0.235
R-Value Work: 0.197
R-Value Observed: 0.199

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Mycobacterial homoserine kinase ThrB

Li, J., Korotkov, K.V.

To be published.

Macromolecule Content

Total Structure Weight: 63.18 kDa
Atom Count: 4,487
Modelled Residue Count: 590
Deposited Residue Count: 616
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Homoserine kinase	A, B	308	Mycobacteroides abscessus ATCC 19977	Mutation(s): 0 Gene Names: thrB, MAB_1437 EC: 2.7.1.39
UniProt
Find proteins for B1MLU6 (Mycobacteroides abscessus (strain ATCC 19977 / DSM 44196 / CCUG 20993 / CIP 104536 / JCM 13569 / NCTC 13031 / TMC 1543 / L948)) Explore B1MLU6 Go to UniProtKB: B1MLU6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	B1MLU6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 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 C [auth A] SDF format, chain E [auth B] MOL2 format, chain C [auth A] MOL2 format, chain E [auth B]	C [auth A], E [auth B]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C₁₀ H₁₇ N₆ O₁₂ P₃ PVKSNHVPLWYQGJ-KQYNXXCUSA-N		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A]	D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.04 Å
R-Value Free: 0.235
R-Value Work: 0.197
R-Value Observed: 0.199
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.35	α = 90
b = 62.7	β = 104.4
c = 84.63	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2018-04-18

Deposition Author(s):

Li, J.

Korotkov, K.V.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	P30GM110787

Revision History (Full details and data files)

Version 1.0: 2018-04-18
Type: Initial release
Version 1.1: 2020-01-01
Changes: Author supporting evidence
Version 1.2: 2023-10-04
Changes: Data collection, Database references, Refinement description

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Help and Resources

6CYZ

Mycobacterial homoserine kinase ThrB in complex with AMPPNP

Mycobacterial homoserine kinase ThrB

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)