7KNP

Crystal structure of Acetyl-CoA synthetase in complex with adenosine-5'-butylphosphate from Cryptococcus neoformans var. grubii serotype A (H99)

PDB DOI: https://doi.org/10.2210/pdb7KNP/pdb

Classification: LIGASE
Organism(s): Cryptococcus neoformans var. grubii H99
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2020-11-05 Released: 2020-12-23
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free: 0.213
R-Value Work: 0.176
R-Value Observed: 0.176

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of Acetyl-CoA synthetase in complex with adenosine-5'-butylphosphate from Cryptococcus neoformans var. grubii serotype A (H99)

Abendroth, J., Fox III, D., Esan, T.E., Hagen, T.J., Krysan, D.J., Lorimer, D.D., Horanyi, P.S., Edwards, T.E.

To be published.

Macromolecule Content

Total Structure Weight: 234.57 kDa
Atom Count: 14,949
Modelled Residue Count: 1,822
Deposited Residue Count: 2,082
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Acetyl-coenzyme A synthetase	A, B, C	694	Cryptococcus neoformans var. grubii H99	Mutation(s): 0 Gene Names: CNAG_00797 EC: 6.2.1.1
UniProt
Find proteins for J9VFT1 (Cryptococcus neoformans var. grubii serotype A (strain H99 / ATCC 208821 / CBS 10515 / FGSC 9487)) Explore J9VFT1 Go to UniProtKB: J9VFT1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	J9VFT1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
WT7 (Subject of Investigation/LOI) Query on WT7 Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain J [auth B] SDF format, chain Q [auth C] MOL2 format, chain D [auth A] MOL2 format, chain J [auth B] MOL2 format, chain Q [auth C]	D [auth A], J [auth B], Q [auth C]	5'-O-[(S)-butoxy(hydroxy)phosphoryl]adenosine C₁₄ H₂₂ N₅ O₇ P VOMQEXIAZJZJAB-IDTAVKCVSA-N		Interactions Focus chain D [auth A] Focus chain J [auth B] Focus chain Q [auth C] Interactions & Density Focus chain D [auth A] Focus chain J [auth B] Focus chain Q [auth C]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain P [auth B] MOL2 format, chain I [auth A] MOL2 format, chain P [auth B]	I [auth A], P [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain I [auth A] Focus chain P [auth B] Interactions & Density Focus chain I [auth A] Focus chain P [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain R [auth C] SDF format, chain S [auth C] SDF format, chain T [auth C] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain R [auth C] MOL2 format, chain S [auth C] MOL2 format, chain T [auth C]	E [auth A] F [auth A] G [auth A] H [auth A] K [auth B] E [auth A], F [auth A], G [auth A], H [auth A], K [auth B], L [auth B], M [auth B], N [auth B], O [auth B], R [auth C], S [auth C], T [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth C] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free: 0.213
R-Value Work: 0.176
R-Value Observed: 0.176
Space Group: P 1 2₁ 1
Diffraction Data: https://doi.org/10.18430/m37knp

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.25	α = 90
b = 184.66	β = 93.84
c = 85.13	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2020-12-23

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2020-12-23
Type: Initial release
Version 1.1: 2020-12-30
Changes: Database references
Version 1.2: 2023-10-18
Changes: Data collection, Database references, Refinement description