5WDG | pdb_00005wdg

Acetolactate Synthase from Klebsiella pneumoniae in Complex with a Reaction Intermediate

PDB DOI: https://doi.org/10.2210/pdb5WDG/pdb

Classification: TRANSFERASE
Organism(s): Klebsiella pneumoniae
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2017-07-05 Released: 2018-07-11
Deposition Author(s): Latta, A.J., Andrews, F.H., McLeish, M.J.
Funding Organization(s): National Science Foundation (NSF, United States)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.12 Å
R-Value Free:
0.247 (Depositor), 0.247 (DCC)
R-Value Work:
0.204 (Depositor), 0.206 (DCC)
R-Value Observed:
0.206 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.0 of the entry. See complete history.

Literature

Acetolactate Synthase from Klebsiella pneumoniae in Complex with Mechanism-Based Inhibitor

Latta, A.J., Andrews, F.H., McLeish, M.J.

To be published.

Macromolecule Content

Total Structure Weight: 126.74 kDa
Atom Count: 8,653
Modeled Residue Count: 1,092
Deposited Residue Count: 1,158
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Acetolactate synthase, catabolic	A, B	579	Klebsiella pneumoniae	Mutation(s): 0 Gene Names: budB, ilvK EC: 2.2.1.6
UniProt
Find proteins for P27696 (Klebsiella pneumoniae) Explore P27696 Go to UniProtKB: P27696
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P27696
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A4Y Query on A4Y Download:Ideal Coordinates CCD File SDF format, chain M [auth B] SDF format, chain G [auth A] MOL2 format, chain M [auth B] MOL2 format, chain G [auth A] mmCIF format, chain M [auth B] mmCIF format, chain G [auth A]	G [auth A], M [auth B]	(2S,3S)-2,3-dihydroxy-3-[(7S,8R,9aS)-8-(2-{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}ethyl)-2,7-dimethyl-5,7,8,10-tetrahydro-9aH-pyrimido[4,5-d][1,3]thiazolo[3,2-a]pyrimidin-9a-yl]-2-methylbutanoic acid C₁₇ H₂₈ N₄ O₁₁ P₂ S AMCOUTJLRZHMEE-PLEBXABZSA-N		Interactions Focus chain G [auth A] Focus chain M [auth B] Interactions & Density Focus chain G [auth A] Focus chain M [auth B]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain L [auth B] MOL2 format, chain F [auth A] MOL2 format, chain L [auth B] mmCIF format, chain F [auth A] mmCIF format, chain L [auth B]	F [auth A], L [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain F [auth A] Focus chain L [auth B] Interactions & Density Focus chain F [auth A] Focus chain L [auth B]
PYR Query on PYR Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain N [auth B] MOL2 format, chain H [auth A] MOL2 format, chain N [auth B] mmCIF format, chain H [auth A] mmCIF format, chain N [auth B]	H [auth A], N [auth B]	PYRUVIC ACID C₃ H₄ O₃ LCTONWCANYUPML-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain N [auth B] Interactions & Density Focus chain H [auth A] Focus chain N [auth B]
MG Query on MG 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 I [auth B] SDF format, chain K [auth B] SDF format, chain J [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain I [auth B] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain I [auth B] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B]	C [auth A] D [auth A] E [auth A] I [auth B] J [auth B] C [auth A], D [auth A], E [auth A], I [auth B], J [auth B], K [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.12 Å
R-Value Free: 0.247 (Depositor), 0.247 (DCC)
R-Value Work: 0.204 (Depositor), 0.206 (DCC)
R-Value Observed: 0.206 (Depositor)

Space Group: I 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.47	α = 90
b = 134.41	β = 95.45
c = 110.745	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data processing
Aimless	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2018-07-11

Deposition Author(s):

Latta, A.J.

Andrews, F.H.

McLeish, M.J.

Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	--

Revision History (Full details and data files)

Version 1.0: 2018-07-11
Type: Initial release
Version 1.1: 2019-11-27
Changes: Author supporting evidence
Version 1.2: 2023-10-04
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 2.0: 2023-11-15
Changes: Atomic model, Data collection

5WDG | pdb_00005wdg

Acetolactate Synthase from Klebsiella pneumoniae in Complex with a Reaction Intermediate

Literature

Acetolactate Synthase from Klebsiella pneumoniae in Complex with Mechanism-Based Inhibitor

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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