6V3M

Crystal structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (IspF) Burkholderia pseudomallei in compomplex with ligand HGN-0961 (BSI110840)

PDB DOI: https://doi.org/10.2210/pdb6V3M/pdb

Classification: LYASE
Organism(s): Burkholderia pseudomallei 1710b
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2019-11-26 Released: 2020-12-09
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free: 0.169
R-Value Work: 0.145
R-Value Observed: 0.145

wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (IspF) Burkholderia pseudomallei in compomplex with ligand HGN-0961 (BSI110840)

Abendroth, J., Yano, J.K., Pierce, P.G., Horn, J.R., Hagen, T.J., Horanyi, P.S., Lorimer, D.D., Edwards, T.E.

To be published.

Macromolecule Content

Total Structure Weight: 60.16 kDa
Atom Count: 4,169
Modelled Residue Count: 480
Deposited Residue Count: 549
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase	A, B, C	183	Burkholderia pseudomallei 1710b	Mutation(s): 0 Gene Names: ispF, BURPS1710b_2511 EC: 4.6.1.12
UniProt
Find proteins for Q3JRA0 (Burkholderia pseudomallei (strain 1710b)) Explore Q3JRA0 Go to UniProtKB: Q3JRA0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q3JRA0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
QOG (Subject of Investigation/LOI) Query on QOG Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain K [auth B] SDF format, chain P [auth C] MOL2 format, chain E [auth A] MOL2 format, chain K [auth B] MOL2 format, chain P [auth C]	E [auth A], K [auth B], P [auth C]	5-{[(propan-2-yl)carbamoyl]amino}-1,3,4-thiadiazole-2-sulfonamide C₆ H₁₁ N₅ O₃ S₂ YLZWSQAIKQWBTO-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain K [auth B] Focus chain P [auth C] Interactions & Density Focus chain E [auth A] Focus chain K [auth B] Focus chain P [auth C]
MLT Query on MLT Download Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A]	I [auth A]	D-MALATE C₄ H₆ O₅ BJEPYKJPYRNKOW-UWTATZPHSA-N		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]
DMS Query on DMS Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain Q [auth C] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain Q [auth C]	F [auth A], G [auth A], L [auth B], M [auth B], Q [auth C]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain Q [auth C] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain Q [auth C]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain J [auth B] SDF format, chain O [auth C] MOL2 format, chain D [auth A] MOL2 format, chain J [auth B] MOL2 format, chain O [auth C]	D [auth A], J [auth B], O [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain J [auth B] Focus chain O [auth C] Interactions & Density Focus chain D [auth A] Focus chain J [auth B] Focus chain O [auth C]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain N [auth B] SDF format, chain R [auth C] MOL2 format, chain H [auth A] MOL2 format, chain N [auth B] MOL2 format, chain R [auth C]	H [auth A], N [auth B], R [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain N [auth B] Focus chain R [auth C] Interactions & Density Focus chain H [auth A] Focus chain N [auth B] Focus chain R [auth C]