5O0Z

Structure of laspartomycin C in complex with geranyl-phosphate

PDB DOI: https://doi.org/10.2210/pdb5O0Z/pdb

Classification: ANTIBIOTIC
Organism(s): Streptomyces viridochromogenes
Mutation(s): No

Deposited: 2017-05-17 Released: 2017-11-15
Deposition Author(s): Vlieg, H.C., Kleijn, L.H.J., Martin, N.I., Janssen, B.J.C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.28 Å
R-Value Free:
0.165 (Depositor), 0.170 (DCC)
R-Value Work:
0.145 (Depositor), 0.150 (DCC)
R-Value Observed:
0.146 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

A High-Resolution Crystal Structure that Reveals Molecular Details of Target Recognition by the Calcium-Dependent Lipopeptide Antibiotic Laspartomycin C.

Kleijn, L.H.J., Vlieg, H.C., Wood, T.M., Sastre Torano, J., Janssen, B.J.C., Martin, N.I.

(2017) Angew Chem Int Ed Engl 56: 16546-16549

PubMed: 29108098 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1002/anie.201709240
Primary Citation of Related Structures:
5O0Z

PubMed Abstract:
The calcium-dependent antibiotics (CDAs) are an important emerging class of antibiotics. The crystal structure of the CDA laspartomycin C in complex with calcium and the ligand geranyl-phosphate at a resolution of 1.28 Å is reported. This is the first crystal structure of a CDA bound to its bacterial target. The structure is also the first to be reported for an antibiotic that binds the essential bacterial phospholipid undecaprenyl phosphate (C ₅₅ -P). These structural insights are of great value in the design of antibiotics capable of exploiting this unique bacterial target.

Organizational Affiliation

Department of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Universiteitsweg 99, 3584, CG, Utrecht, The Netherlands.

Macromolecule Content

Total Structure Weight: 3.3 kDa
Atom Count: 213
Modelled Residue Count: 24
Deposited Residue Count: 24
Unique protein chains: 1

Macromolecules

Find similar proteins by: Sequence | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Laspartomycin C	A, B	12	Streptomyces viridochromogenes	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
9GB Query on 9GB Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain I [auth B] MOL2 format, chain C [auth A] MOL2 format, chain I [auth B] mmCIF format, chain C [auth A] mmCIF format, chain I [auth B]	C [auth A], I [auth B]	[(~{E})-3-methylhex-2-enyl] dihydrogen phosphate C₇ H₁₅ O₄ P QFTXOINSFIOLQI-FNORWQNLSA-N		Interactions Focus chain C [auth A] Focus chain I [auth B] Interactions & Density Focus chain C [auth A] Focus chain I [auth B]
ACY Query on ACY Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain L [auth B] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain L [auth B] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain L [auth B]	G [auth A], H [auth A], L [auth B]	ACETIC ACID C₂ H₄ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain L [auth B] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain L [auth B]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain J [auth B] SDF format, chain K [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B]	D [auth A], E [auth A], J [auth B], K [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain J [auth B] Focus chain K [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain J [auth B] Focus chain K [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
DNP Query on DNP	A, B	L-PEPTIDE LINKING	C₃ H₉ N₂ O₂		ALA

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 1
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_002234 Query on PRD_002234	A, B	Laspartomycin C	Lipopeptide / Antibiotic		Interactions Focus chain A Focus chain B Interactions & Density Focus chain A Focus chain B

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.28 Å
R-Value Free: 0.165 (Depositor), 0.170 (DCC)
R-Value Work: 0.145 (Depositor), 0.150 (DCC)
R-Value Observed: 0.146 (Depositor)

Space Group: P 4₃ 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.933	α = 90
b = 56.933	β = 90
c = 56.933	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
iMOSFLM	data reduction
Aimless	data scaling
SHELXCD	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2017-11-15

Deposition Author(s):

Funding Organization	Location	Grant Number
	Netherlands	--

Revision History (Full details and data files)

Version 1.0: 2017-11-15
Type: Initial release
Version 1.1: 2017-12-13
Changes: Database references
Version 1.2: 2018-01-03
Changes: Database references
Version 1.3: 2019-10-16
Changes: Data collection
Version 2.0: 2024-08-07
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary